HEADER ISOMERASE 24-DEC-12 4IJZ TITLE CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE EPIMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAP EPIMERASE; COMPND 5 EC: 5.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DAPF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS DAP EPIMERASE-LIKE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.HOR,R.C.J.DOBSON,C.A.HUTTON,M.A.PERUGINI REVDAT 3 17-APR-13 4IJZ 1 JRNL REVDAT 2 06-MAR-13 4IJZ 1 JRNL REVDAT 1 20-FEB-13 4IJZ 0 JRNL AUTH L.HOR,R.C.J.DOBSON,M.T.DOWNTON,J.WAGNER,C.A.HUTTON, JRNL AUTH 2 M.A.PERUGINI JRNL TITL DIMERIZATION OF BACTERIAL DIAMINOPIMELATE EPIMERASE IS JRNL TITL 2 ESSENTIAL FOR CATALYSIS JRNL REF J.BIOL.CHEM. V. 288 9238 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23426375 JRNL DOI 10.1074/JBC.M113.450148 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 47638 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1949 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2889 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 145 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4244 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 516 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : -0.00000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.897 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4394 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5960 ; 1.640 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 561 ; 6.518 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;33.118 ;23.196 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 711 ;13.096 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;19.601 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3446 ; 0.008 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 6 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 111 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0280 -9.6533 10.1530 REMARK 3 T TENSOR REMARK 3 T11: 0.0500 T22: 0.0503 REMARK 3 T33: 0.0527 T12: 0.0273 REMARK 3 T13: -0.0048 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.6149 L22: 1.0657 REMARK 3 L33: 0.7388 L12: -0.3876 REMARK 3 L13: -0.2281 L23: 0.7101 REMARK 3 S TENSOR REMARK 3 S11: -0.0521 S12: -0.0582 S13: 0.0294 REMARK 3 S21: 0.0509 S22: 0.0669 S23: -0.0395 REMARK 3 S31: 0.0804 S32: 0.0290 S33: -0.0148 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 : A 112 A 261 REMARK 3 ORIGIN FOR THE GROUP (A): 34.1466 -15.7063 16.2901 REMARK 3 T TENSOR REMARK 3 T11: 0.0287 T22: 0.0631 REMARK 3 T33: 0.0776 T12: 0.0184 REMARK 3 T13: -0.0151 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.8036 L22: 1.8121 REMARK 3 L33: 0.4084 L12: -1.3182 REMARK 3 L13: 0.6198 L23: -0.7934 REMARK 3 S TENSOR REMARK 3 S11: -0.0935 S12: -0.0968 S13: -0.0740 REMARK 3 S21: -0.0483 S22: 0.0484 S23: 0.0485 REMARK 3 S31: -0.0023 S32: -0.0180 S33: 0.0451 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 262 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): 8.2921 -6.7960 -1.0399 REMARK 3 T TENSOR REMARK 3 T11: 0.1098 T22: 0.1066 REMARK 3 T33: 0.1214 T12: -0.0075 REMARK 3 T13: -0.0962 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 2.4766 L22: 2.8168 REMARK 3 L33: 2.6354 L12: -1.6202 REMARK 3 L13: 2.3045 L23: -2.4345 REMARK 3 S TENSOR REMARK 3 S11: -0.2073 S12: -0.0437 S13: 0.2443 REMARK 3 S21: -0.2337 S22: 0.1782 S23: 0.2209 REMARK 3 S31: 0.0017 S32: -0.1030 S33: 0.0291 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 112 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2161 -9.4398 -21.4323 REMARK 3 T TENSOR REMARK 3 T11: 0.0841 T22: 0.0462 REMARK 3 T33: 0.0484 T12: 0.0105 REMARK 3 T13: 0.0137 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.7209 L22: 0.3816 REMARK 3 L33: 0.4652 L12: -0.0724 REMARK 3 L13: -0.0096 L23: 0.4042 REMARK 3 S TENSOR REMARK 3 S11: -0.0102 S12: 0.0122 S13: -0.0658 REMARK 3 S21: -0.0831 S22: 0.0150 S23: -0.0199 REMARK 3 S31: -0.0800 S32: -0.0138 S33: -0.0047 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 113 B 228 REMARK 3 ORIGIN FOR THE GROUP (A): 15.8216 -34.5036 -27.5011 REMARK 3 T TENSOR REMARK 3 T11: 0.0791 T22: 0.0515 REMARK 3 T33: 0.0621 T12: 0.0302 REMARK 3 T13: 0.0084 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 1.3660 L22: 1.6006 REMARK 3 L33: 0.8691 L12: -1.2535 REMARK 3 L13: -1.0441 L23: 0.9241 REMARK 3 S TENSOR REMARK 3 S11: -0.0673 S12: -0.1157 S13: 0.1478 REMARK 3 S21: 0.1741 S22: 0.1408 S23: -0.1729 REMARK 3 S31: 0.1022 S32: 0.1066 S33: -0.0736 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 229 B 275 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8611 -24.7342 -24.1872 REMARK 3 T TENSOR REMARK 3 T11: 0.0575 T22: 0.0329 REMARK 3 T33: 0.0366 T12: 0.0056 REMARK 3 T13: 0.0219 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 0.4406 L22: 1.6389 REMARK 3 L33: 1.2974 L12: -0.1943 REMARK 3 L13: -0.0598 L23: 1.4293 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: 0.0126 S13: -0.0463 REMARK 3 S21: 0.0670 S22: -0.0746 S23: 0.0927 REMARK 3 S31: 0.0484 S32: -0.0686 S33: 0.0885 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 4IJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-12. REMARK 100 THE RCSB ID CODE IS RCSB076847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47663 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 179.618 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : 0.33900 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM NITRATE, PEG 3350, BIS-TRIS REMARK 280 PROPANE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.80900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.69000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.90450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.69000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.69000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 134.71350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.69000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.69000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.90450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.69000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 134.71350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 89.80900 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A 275 REMARK 465 HIS A 276 REMARK 465 HIS A 277 REMARK 465 HIS A 278 REMARK 465 HIS A 279 REMARK 465 HIS A 280 REMARK 465 HIS B 276 REMARK 465 HIS B 277 REMARK 465 HIS B 278 REMARK 465 HIS B 279 REMARK 465 HIS B 280 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 GLN A 72 CG CD OE1 NE2 REMARK 470 LYS A 198 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 648 O HOH B 658 1.84 REMARK 500 O HOH B 499 O HOH B 562 2.18 REMARK 500 OE2 GLU B 208 OG1 THR B 214 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 646 O HOH B 533 3545 2.01 REMARK 500 O HOH A 574 O HOH B 634 7555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 7 CG HIS A 7 CD2 0.059 REMARK 500 HIS B 182 CG HIS B 182 CD2 0.066 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 71 -75.33 -75.83 REMARK 500 ALA A 144 -130.42 52.37 REMARK 500 ARG A 188 -179.08 63.24 REMARK 500 ALA A 216 118.29 -162.04 REMARK 500 LEU B 9 -19.56 79.78 REMARK 500 ALA B 144 -133.43 59.44 REMARK 500 ARG B 188 177.07 66.32 REMARK 500 ALA B 211 -15.73 -155.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 540 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 587 DISTANCE = 5.12 ANGSTROMS REMARK 525 HOH A 616 DISTANCE = 5.16 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IK0 RELATED DB: PDB DBREF 4IJZ A 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 DBREF 4IJZ B 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 SEQADV 4IJZ HIS A 275 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS A 276 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS A 277 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS A 278 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS A 279 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS A 280 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 275 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 276 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 277 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 278 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 279 UNP P0A6K1 EXPRESSION TAG SEQADV 4IJZ HIS B 280 UNP P0A6K1 EXPRESSION TAG SEQRES 1 A 280 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 A 280 MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SER SEQRES 3 A 280 PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU GLY SEQRES 4 A 280 VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO TYR SEQRES 5 A 280 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 A 280 ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA ARG SEQRES 7 A 280 CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR ASN SEQRES 8 A 280 LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG MET SEQRES 9 A 280 VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL ASN SEQRES 10 A 280 MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO PHE SEQRES 11 A 280 ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG ALA SEQRES 12 A 280 ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET GLY SEQRES 13 A 280 ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP THR SEQRES 14 A 280 ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER HIS SEQRES 15 A 280 GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET GLN SEQRES 16 A 280 VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR GLU SEQRES 17 A 280 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 A 280 CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU LEU SEQRES 19 A 280 ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG LEU SEQRES 20 A 280 ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR MET SEQRES 21 A 280 THR GLY PRO ALA VAL HIS VAL TYR ASP GLY PHE ILE HIS SEQRES 22 A 280 LEU HIS HIS HIS HIS HIS HIS SEQRES 1 B 280 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 B 280 MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SER SEQRES 3 B 280 PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU GLY SEQRES 4 B 280 VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO TYR SEQRES 5 B 280 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 B 280 ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA ARG SEQRES 7 B 280 CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR ASN SEQRES 8 B 280 LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG MET SEQRES 9 B 280 VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL ASN SEQRES 10 B 280 MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO PHE SEQRES 11 B 280 ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG ALA SEQRES 12 B 280 ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET GLY SEQRES 13 B 280 ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP THR SEQRES 14 B 280 ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER HIS SEQRES 15 B 280 GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET GLN SEQRES 16 B 280 VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR GLU SEQRES 17 B 280 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 B 280 CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU LEU SEQRES 19 B 280 ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG LEU SEQRES 20 B 280 ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR MET SEQRES 21 B 280 THR GLY PRO ALA VAL HIS VAL TYR ASP GLY PHE ILE HIS SEQRES 22 B 280 LEU HIS HIS HIS HIS HIS HIS HET NO3 A 301 4 HET NO3 A 302 4 HET NO3 B 301 4 HETNAM NO3 NITRATE ION FORMUL 3 NO3 3(N O3 1-) FORMUL 6 HOH *516(H2 O) HELIX 1 1 SER A 26 ASP A 35 1 10 HELIX 2 2 CYS A 73 LYS A 87 1 15 HELIX 3 3 GLU A 124 VAL A 128 5 5 HELIX 4 4 ASP A 166 ALA A 170 5 5 HELIX 5 5 ALA A 171 SER A 181 1 11 HELIX 6 6 CYS A 217 GLN A 231 1 15 HELIX 7 7 SER B 26 ASP B 35 1 10 HELIX 8 8 GLY B 76 LYS B 87 1 12 HELIX 9 9 GLU B 124 VAL B 128 5 5 HELIX 10 10 ASP B 166 ALA B 170 5 5 HELIX 11 11 ALA B 171 SER B 181 1 11 HELIX 12 12 CYS B 217 GLN B 231 1 15 SHEET 1 A 6 TYR B 139 ALA B 143 0 SHEET 2 A 6 GLN B 146 SER B 154 -1 O ILE B 148 N MET B 141 SHEET 3 A 6 PRO B 158 GLN B 163 -1 O VAL B 161 N GLY B 151 SHEET 4 A 6 ASN B 190 LYS B 198 1 O GLY B 192 N CYS B 160 SHEET 5 A 6 HIS B 201 GLU B 208 -1 O TYR B 207 N ILE B 191 SHEET 6 A 6 GLY B 212 THR B 214 -1 N GLY B 212 O GLU B 208 SHEET 1 B10 GLY B 212 THR B 214 0 SHEET 2 B10 HIS B 201 GLU B 208 -1 O GLU B 208 N GLY B 212 SHEET 3 B10 GLU B 237 LEU B 242 1 O GLU B 241 N LEU B 204 SHEET 4 B10 GLY B 245 TRP B 251 -1 O LEU B 247 N VAL B 240 SHEET 5 B10 LEU B 258 GLY B 262 -1 O THR B 261 N ASP B 248 SHEET 6 B10 VAL B 114 ASN B 117 -1 N VAL B 116 O MET B 260 SHEET 7 B10 GLY B 102 VAL B 108 -1 N THR B 107 O ARG B 115 SHEET 8 B10 ASP B 94 THR B 99 -1 N ILE B 95 O LEU B 106 SHEET 9 B10 PHE B 58 ASN B 64 1 N TYR B 60 O SER B 98 SHEET 10 B10 GLU B 69 VAL B 70 -1 O VAL B 70 N ILE B 62 SHEET 1 C12 GLU B 69 VAL B 70 0 SHEET 2 C12 PHE B 58 ASN B 64 -1 N ILE B 62 O VAL B 70 SHEET 3 C12 GLN B 44 GLU B 49 -1 N VAL B 47 O ARG B 61 SHEET 4 C12 ASP B 12 ASP B 17 1 N MET B 14 O LEU B 46 SHEET 5 C12 GLN B 2 HIS B 7 -1 N SER B 4 O VAL B 15 SHEET 6 C12 VAL B 265 PHE B 271 -1 O GLY B 270 N PHE B 3 SHEET 7 C12 VAL A 265 ILE A 272 -1 N ASP A 269 O PHE B 271 SHEET 8 C12 GLN A 2 GLY A 8 -1 N LYS A 5 O TYR A 268 SHEET 9 C12 ASN A 11 ASP A 17 -1 O VAL A 15 N SER A 4 SHEET 10 C12 GLN A 44 GLU A 49 1 O VAL A 48 N VAL A 16 SHEET 11 C12 PHE A 58 ASN A 64 -1 O HIS A 59 N GLU A 49 SHEET 12 C12 GLU A 69 VAL A 70 -1 O VAL A 70 N ILE A 62 SHEET 1 D13 GLU A 69 VAL A 70 0 SHEET 2 D13 PHE A 58 ASN A 64 -1 N ILE A 62 O VAL A 70 SHEET 3 D13 ASP A 94 THR A 99 1 O SER A 98 N TYR A 60 SHEET 4 D13 GLY A 102 VAL A 108 -1 O LEU A 106 N ILE A 95 SHEET 5 D13 VAL A 114 ASN A 117 -1 O ARG A 115 N THR A 107 SHEET 6 D13 LEU A 258 GLY A 262 -1 O MET A 260 N VAL A 116 SHEET 7 D13 GLY A 245 TRP A 251 -1 N ASP A 248 O THR A 261 SHEET 8 D13 GLU A 237 LEU A 242 -1 N VAL A 240 O LEU A 247 SHEET 9 D13 HIS A 201 GLU A 208 1 N ILE A 202 O ARG A 239 SHEET 10 D13 ASN A 190 LYS A 198 -1 N ILE A 191 O TYR A 207 SHEET 11 D13 PRO A 158 VAL A 164 1 N CYS A 160 O GLY A 192 SHEET 12 D13 GLN A 146 SER A 154 -1 N GLY A 151 O VAL A 161 SHEET 13 D13 TYR A 139 ALA A 143 -1 N MET A 141 O ILE A 148 SHEET 1 E 6 GLY A 212 GLU A 213 0 SHEET 2 E 6 HIS A 201 GLU A 208 -1 N GLU A 208 O GLY A 212 SHEET 3 E 6 ASN A 190 LYS A 198 -1 N ILE A 191 O TYR A 207 SHEET 4 E 6 PRO A 158 VAL A 164 1 N CYS A 160 O GLY A 192 SHEET 5 E 6 GLN A 146 SER A 154 -1 N GLY A 151 O VAL A 161 SHEET 6 E 6 TYR A 139 ALA A 143 -1 N MET A 141 O ILE A 148 CISPEP 1 VAL A 128 PRO A 129 0 -6.86 CISPEP 2 HIS A 273 LEU A 274 0 14.80 CISPEP 3 VAL B 128 PRO B 129 0 -9.49 SITE 1 AC1 9 ALA A 132 ASN A 133 LYS A 134 TYR A 139 SITE 2 AC1 9 ARG A 184 HOH A 516 PHE B 24 PHE B 25 SITE 3 AC1 9 SER B 26 SITE 1 AC2 4 VAL A 23 GLU A 49 HOH A 437 ARG B 142 SITE 1 AC3 10 PHE A 24 PHE A 25 SER A 26 ALA B 132 SITE 2 AC3 10 ASN B 133 LYS B 134 TYR B 139 ARG B 184 SITE 3 AC3 10 HOH B 427 HOH B 551 CRYST1 89.380 89.380 179.618 90.00 90.00 90.00 P 41 21 2 16 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 0.011188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005567 0.00000 MASTER 491 0 3 12 47 0 7 6 0 0 0 44 END