HEADER LYASE 08-JUL-09 3I7S TITLE DIHYDRODIPICOLINATE SYNTHASE MUTANT - K161A - WITH THE SUBSTRATE TITLE 2 PYRUVATE BOUND IN THE ACTIVE SITE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: DIHYDRODIPICOLINATE SYNTHASE; COMPND 5 SYNONYM: DHDPS; COMPND 6 EC: 4.2.1.52; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: B2478, DAPA, JW2463; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: E. COLI BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJG001 KEYWDS DIHYDRODIPICOLINATE SYNTHYASE, LYSINE BIOSYNTHESIS, AMINO-ACID KEYWDS 2 BIOSYNTHESIS, DIAMINOPIMELATE BIOSYNTHESIS, LYASE, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR R.C.J.DOBSON,G.B.JAMESON,J.A.GERRARD,T.P.SOARES DA COSTA REVDAT 4 13-OCT-21 3I7S 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3I7S 1 VERSN REVDAT 2 07-JUL-10 3I7S 1 JRNL REVDAT 1 14-APR-10 3I7S 0 JRNL AUTH T.P.SOARES DA COSTA,A.C.MUSCROFT-TAYLOR,R.C.DOBSON, JRNL AUTH 2 S.R.DEVENISH,G.B.JAMESON,J.A.GERRARD JRNL TITL HOW ESSENTIAL IS THE 'ESSENTIAL' ACTIVE-SITE LYSINE IN JRNL TITL 2 DIHYDRODIPICOLINATE SYNTHASE? JRNL REF BIOCHIMIE V. 92 837 2010 JRNL REFN ISSN 0300-9084 JRNL PMID 20353808 JRNL DOI 10.1016/J.BIOCHI.2010.03.004 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 37802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2019 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2794 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : -0.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.228 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4504 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6113 ; 1.364 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 6.131 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;37.693 ;24.566 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;15.394 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.417 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 731 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3311 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2906 ; 0.561 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4688 ; 1.086 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 2.013 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 3.312 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1620 32.3130 -11.9510 REMARK 3 T TENSOR REMARK 3 T11: 0.0435 T22: 0.0215 REMARK 3 T33: 0.0276 T12: -0.0230 REMARK 3 T13: -0.0307 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 0.3457 L22: 0.5233 REMARK 3 L33: 0.6722 L12: -0.0375 REMARK 3 L13: 0.1343 L23: 0.0137 REMARK 3 S TENSOR REMARK 3 S11: 0.0868 S12: -0.0133 S13: -0.0668 REMARK 3 S21: -0.0199 S22: 0.0116 S23: 0.0070 REMARK 3 S31: 0.0550 S32: -0.0633 S33: -0.0984 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 292 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8400 61.5350 -2.3280 REMARK 3 T TENSOR REMARK 3 T11: 0.0329 T22: 0.0306 REMARK 3 T33: 0.0073 T12: -0.0030 REMARK 3 T13: -0.0031 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.4387 L22: 0.3111 REMARK 3 L33: 0.4704 L12: 0.0097 REMARK 3 L13: -0.0107 L23: 0.2416 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0000 S13: 0.0288 REMARK 3 S21: 0.0023 S22: 0.0121 S23: 0.0115 REMARK 3 S31: -0.0100 S32: -0.0265 S33: -0.0250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3I7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39830 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 32.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.420 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 7.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.27 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M POTASSIUM PHOSPHATE, PH 10, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 276K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.83333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.66667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.66667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.83333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A TETRAMER, GENERATED FROM THE DIMER REMARK 300 IN THE ASSYMETRIC UNIT. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 312 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 306 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 212 CD NE CZ NH1 NH2 REMARK 470 LYS A 219 CD CE NZ REMARK 470 ARG B 161 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 107 -44.76 74.88 REMARK 500 ALA A 210 46.72 -145.30 REMARK 500 THR B 77 16.14 -140.90 REMARK 500 TYR B 107 -52.53 77.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 296 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 48 O REMARK 620 2 ALA A 49 O 74.4 REMARK 620 3 LEU A 51 O 74.5 101.5 REMARK 620 4 GOL A 297 O3 114.2 81.4 171.3 REMARK 620 5 GOL A 297 O3 122.1 66.4 152.0 23.0 REMARK 620 6 HOH A 360 O 74.5 110.7 126.4 58.8 81.4 REMARK 620 7 HOH A 361 O 135.2 66.3 92.5 81.1 59.6 139.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 295 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 84.7 REMARK 620 3 LYS A 155 O 146.6 63.9 REMARK 620 4 ILE A 157 O 99.2 82.8 88.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 296 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 301 O REMARK 620 2 SER B 48 O 108.4 REMARK 620 3 ALA B 49 O 51.3 66.5 REMARK 620 4 LEU B 51 O 134.0 71.3 92.1 REMARK 620 5 HOH B 398 O 91.3 156.5 137.0 104.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 299 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 152 O REMARK 620 2 VAL B 154 O 81.6 REMARK 620 3 LYS B 155 O 146.4 67.6 REMARK 620 4 ILE B 157 O 98.5 82.6 90.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR A 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 294 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 296 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 297 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 298 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I7Q RELATED DB: PDB REMARK 900 RELATED ID: 3I7R RELATED DB: PDB DBREF 3I7S A 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 DBREF 3I7S B 1 292 UNP P0A6L2 DAPA_ECOLI 1 292 SEQADV 3I7S ARG A 161 UNP P0A6L2 LYS 161 ENGINEERED MUTATION SEQADV 3I7S ARG B 161 UNP P0A6L2 LYS 161 ENGINEERED MUTATION SEQRES 1 A 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 A 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 A 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 A 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN SEQRES 5 A 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 A 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 A 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 A 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 A 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 A 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 A 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 A 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 A 292 ILE ILE GLY ILE ARG GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 A 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 A 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 A 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 A 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 A 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 A 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 A 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 A 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 A 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 A 292 LYS HIS ALA GLY LEU LEU SEQRES 1 B 292 MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO MET SEQRES 2 B 292 ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS LYS SEQRES 3 B 292 LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA ILE SEQRES 4 B 292 VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU ASN SEQRES 5 B 292 HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU ASP SEQRES 6 B 292 LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR GLY SEQRES 7 B 292 ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN ARG SEQRES 8 B 292 PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL THR SEQRES 9 B 292 PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR GLN SEQRES 10 B 292 HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO GLN SEQRES 11 B 292 ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP LEU SEQRES 12 B 292 LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS ASN SEQRES 13 B 292 ILE ILE GLY ILE ARG GLU ALA THR GLY ASN LEU THR ARG SEQRES 14 B 292 VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE VAL SEQRES 15 B 292 LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE MET SEQRES 16 B 292 GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA ASN SEQRES 17 B 292 VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU ALA SEQRES 18 B 292 ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN GLN SEQRES 19 B 292 ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU PRO SEQRES 20 B 292 ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU GLY SEQRES 21 B 292 LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR PRO SEQRES 22 B 292 ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA LEU SEQRES 23 B 292 LYS HIS ALA GLY LEU LEU HET GOL A 293 6 HET GOL A 294 6 HET K A 295 1 HET K A 296 1 HET GOL A 297 12 HET PYR A 298 6 HET PO4 A 299 5 HET PO4 A 300 5 HET GOL B 293 6 HET GOL B 294 6 HET K B 295 1 HET K B 296 1 HET GOL B 297 6 HET K B 298 1 HET K B 299 1 HET GOL B 300 6 HET GOL B 301 6 HET PYR B 302 6 HET PO4 B 303 5 HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETNAM PYR PYRUVIC ACID HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 8(C3 H8 O3) FORMUL 5 K 6(K 1+) FORMUL 8 PYR 2(C3 H4 O3) FORMUL 9 PO4 3(O4 P 3-) FORMUL 22 HOH *170(H2 O) HELIX 1 1 CYS A 20 GLY A 35 1 16 HELIX 2 2 GLU A 47 LEU A 51 5 5 HELIX 3 3 ASN A 52 ASP A 68 1 17 HELIX 4 4 ALA A 81 ARG A 91 1 11 HELIX 5 5 SER A 111 HIS A 125 1 15 HELIX 6 6 VAL A 135 GLY A 140 1 6 HELIX 7 7 LEU A 144 ALA A 152 1 9 HELIX 8 8 THR A 168 GLU A 175 1 8 HELIX 9 9 ASP A 187 ALA A 189 5 3 HELIX 10 10 SER A 190 LEU A 197 1 8 HELIX 11 11 VAL A 205 VAL A 209 5 5 HELIX 12 12 ALA A 210 GLU A 223 1 14 HELIX 13 13 HIS A 225 LEU A 243 1 19 HELIX 14 14 PRO A 249 LEU A 259 1 11 HELIX 15 15 THR A 275 ALA A 289 1 15 HELIX 16 16 CYS B 20 GLY B 35 1 16 HELIX 17 17 GLY B 43 LEU B 51 5 9 HELIX 18 18 ASN B 52 ASP B 68 1 17 HELIX 19 19 ALA B 81 ARG B 91 1 11 HELIX 20 20 SER B 111 HIS B 125 1 15 HELIX 21 21 VAL B 135 GLY B 140 1 6 HELIX 22 22 LEU B 144 LYS B 153 1 10 HELIX 23 23 THR B 168 VAL B 177 1 10 HELIX 24 24 ASP B 187 ALA B 189 5 3 HELIX 25 25 SER B 190 LEU B 197 1 8 HELIX 26 26 VAL B 205 VAL B 209 5 5 HELIX 27 27 ALA B 210 GLY B 224 1 15 HELIX 28 28 HIS B 225 LEU B 243 1 19 HELIX 29 29 PRO B 249 LEU B 259 1 11 HELIX 30 30 THR B 275 ALA B 289 1 15 SHEET 1 A 9 GLY A 4 ALA A 8 0 SHEET 2 A 9 ALA A 38 SER A 41 1 O VAL A 40 N VAL A 7 SHEET 3 A 9 VAL A 73 GLY A 76 1 O ILE A 74 N ILE A 39 SHEET 4 A 9 GLY A 99 VAL A 103 1 O LEU A 101 N ALA A 75 SHEET 5 A 9 GLN A 130 ASN A 134 1 O ILE A 131 N CYS A 100 SHEET 6 A 9 ILE A 157 GLU A 162 1 O ARG A 161 N LEU A 132 SHEET 7 A 9 VAL A 182 SER A 185 1 O LEU A 184 N ILE A 160 SHEET 8 A 9 GLY A 201 SER A 204 1 O ILE A 203 N SER A 185 SHEET 9 A 9 GLY A 4 ALA A 8 1 N ILE A 6 O SER A 204 SHEET 1 B 9 GLY B 4 ALA B 8 0 SHEET 2 B 9 ALA B 38 SER B 41 1 O VAL B 40 N VAL B 7 SHEET 3 B 9 VAL B 73 GLY B 76 1 O ILE B 74 N ILE B 39 SHEET 4 B 9 GLY B 99 VAL B 103 1 O LEU B 101 N ALA B 75 SHEET 5 B 9 GLN B 130 ASN B 134 1 O ILE B 131 N CYS B 100 SHEET 6 B 9 ILE B 157 GLU B 162 1 O ARG B 161 N LEU B 132 SHEET 7 B 9 VAL B 182 SER B 185 1 O LEU B 184 N GLU B 162 SHEET 8 B 9 GLY B 201 SER B 204 1 O ILE B 203 N SER B 185 SHEET 9 B 9 GLY B 4 ALA B 8 1 N ILE B 6 O SER B 204 LINK O SER A 48 K K A 296 1555 1555 2.90 LINK O ALA A 49 K K A 296 1555 1555 3.01 LINK O LEU A 51 K K A 296 1555 1555 2.69 LINK O ALA A 152 K K A 295 1555 1555 2.84 LINK O VAL A 154 K K A 295 1555 1555 2.76 LINK O LYS A 155 K K A 295 1555 1555 3.24 LINK O ILE A 157 K K A 295 1555 1555 2.71 LINK K K A 296 O3 AGOL A 297 1555 1555 2.86 LINK K K A 296 O3 BGOL A 297 1555 1555 3.00 LINK K K A 296 O HOH A 360 1555 1555 2.49 LINK K K A 296 O HOH A 361 1555 1555 2.77 LINK O HOH A 301 K K B 296 1555 1555 3.09 LINK O SER B 48 K K B 296 1555 1555 3.05 LINK O ALA B 49 K K B 296 1555 1555 3.29 LINK O LEU B 51 K K B 296 1555 1555 2.80 LINK OE1 GLU B 84 K K B 298 1555 1555 3.21 LINK O ALA B 152 K K B 299 1555 1555 2.58 LINK O VAL B 154 K K B 299 1555 1555 2.59 LINK O LYS B 155 K K B 299 1555 1555 3.37 LINK O ILE B 157 K K B 299 1555 1555 2.72 LINK K K B 296 O HOH B 398 1555 1555 2.99 CISPEP 1 ASN A 248 PRO A 249 0 9.14 CISPEP 2 LEU A 269 PRO A 270 0 12.89 CISPEP 3 ASN B 248 PRO B 249 0 9.10 CISPEP 4 LEU B 269 PRO B 270 0 12.00 SITE 1 AC1 10 SER A 48 ALA A 49 GLY A 78 VAL A 103 SITE 2 AC1 10 TYR A 106 GOL A 297 HOH A 337 HOH A 360 SITE 3 AC1 10 ASN B 80 TYR B 107 SITE 1 AC2 3 LYS A 174 GLU A 175 VAL A 177 SITE 1 AC3 4 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 1 AC4 6 SER A 48 ALA A 49 LEU A 51 GOL A 297 SITE 2 AC4 6 HOH A 360 HOH A 361 SITE 1 AC5 13 ALA A 49 ASN A 80 TYR A 106 GOL A 293 SITE 2 AC5 13 K A 296 HOH A 301 HOH A 321 HOH A 331 SITE 3 AC5 13 HOH A 360 HOH A 361 ASN B 80 TYR B 106 SITE 4 AC5 13 GOL B 293 SITE 1 AC6 10 ALA A 8 GLY A 43 THR A 44 THR A 45 SITE 2 AC6 10 LEU A 101 TYR A 133 HOH A 349 HOH A 350 SITE 3 AC6 10 HOH A 351 HOH A 363 SITE 1 AC7 2 ARG A 21 LYS A 25 SITE 1 AC8 1 ARG A 109 SITE 1 AC9 6 ASN A 80 TYR A 107 GOL A 297 SER B 48 SITE 2 AC9 6 ALA B 49 TYR B 106 SITE 1 BC1 7 ASP B 29 VAL B 32 ALA B 33 ARG B 70 SITE 2 BC1 7 HIS B 125 K B 295 GOL B 300 SITE 1 BC2 2 HIS B 125 GOL B 294 SITE 1 BC3 5 HOH A 301 SER B 48 ALA B 49 LEU B 51 SITE 2 BC3 5 HOH B 398 SITE 1 BC4 8 PRO B 110 SER B 111 GLN B 112 CYS B 141 SITE 2 BC4 8 ASP B 142 LEU B 144 GOL B 301 HOH B 322 SITE 1 BC5 1 GLU B 84 SITE 1 BC6 4 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 1 BC7 4 LYS B 26 ILE B 86 HIS B 125 GOL B 294 SITE 1 BC8 3 SER B 111 GLN B 112 GOL B 297 SITE 1 BC9 9 GLY B 43 THR B 44 THR B 45 LEU B 101 SITE 2 BC9 9 TYR B 133 HOH B 379 HOH B 383 HOH B 385 SITE 3 BC9 9 HOH B 403 SITE 1 CC1 1 ARG B 109 CRYST1 120.881 120.881 110.500 90.00 90.00 120.00 P 31 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008273 0.004776 0.000000 0.00000 SCALE2 0.000000 0.009552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009050 0.00000 MASTER 466 0 19 30 18 0 33 6 0 0 0 46 END