10 20 30 40 50 60 70 80 3DIE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 20-JUN-08 3DIE
TITLE DOMAIN SWAPPING OF STAPHYLOCOCCUS AUREUS THIOREDOXIN W28A TITLE 2 MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRX; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: TRXA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (AI); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET14B
KEYWDS ELECTRON TRANSPORT, SWAP DOMAIN, REDOX ENZYMOLOGY, KEYWDS 2 OXIDOREDUCTASE, REDOX-ACTIVE CENTER, TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR S.MARTINEZ-RODRIGUEZ,R.LORIS,J.MESSENS
REVDAT 1 24-MAR-09 3DIE 0
JRNL AUTH A.GARCIA-PINO,S.MARTINEZ-RODRIGUEZ,K.WAHNI,L.WYNS, JRNL AUTH 2 R.LORIS,J.MESSENS JRNL TITL COUPLING OF DOMAIN SWAPPING TO KINETIC STABILITY JRNL TITL 2 IN A THIOREDOXIN MUTANT JRNL REF J.MOL.BIOL. V. 385 1590 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19071139 JRNL DOI 10.1016/J.JMB.2008.11.040
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21599 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1580 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1539 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : 0.25000 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): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.319 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1569 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2149 ; 1.648 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ;20.090 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;30.937 ;26.727 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 231 ;13.764 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 261 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1176 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 627 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1129 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.270 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.353 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 31 ; 0.253 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.274 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.571 ; 0.200 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): 1083 ; 1.078 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1705 ; 1.446 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 545 ; 2.606 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 444 ; 4.081 ; 4.500 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 : NULL 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3DIE COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB048075.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.8152 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 61.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : 0.19000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 56.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%(V/V) POLYETHYLENE GLYCOL 400, REMARK 280 0.1M SODIUM ACETATE PH 4.6, 0.1M CADMIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 44.35150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.22550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.35150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.22550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 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 5 CD CE NZ REMARK 470 LYS A 33 CG CD CE NZ REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 49 CE NZ REMARK 470 LYS A 66 CD CE NZ REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 GLN A 82 OE1 NE2 REMARK 470 LYS A 86 CE NZ REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 LYS A 102 NZ REMARK 470 MET B 1 SD CE REMARK 470 VAL B 4 CG1 CG2 REMARK 470 LYS B 5 NZ REMARK 470 ASP B 12 OD1 OD2 REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 470 THR B 27 CG2 REMARK 470 LYS B 33 CD CE NZ REMARK 470 LYS B 49 CE NZ REMARK 470 LYS B 66 CD CE NZ REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 GLN B 82 CG CD OE1 NE2 REMARK 470 LYS B 86 CE NZ REMARK 470 LYS B 93 NZ REMARK 470 GLU B 94 CB CG CD OE1 OE2 REMARK 470 GLU B 98 CG CD OE1 OE2 REMARK 470 LYS B 102 CG CD 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 CD CD A 107 O HOH A 188 1.57 REMARK 500 O HOH A 180 O HOH A 181 1.79 REMARK 500 OD1 ASP B 45 O HOH B 167 2.08 REMARK 500 OE2 GLU A 41 O HOH A 132 2.09 REMARK 500 NE2 HIS B 0 O HOH A 132 2.17 REMARK 500 OD2 ASP A 58 O HOH A 158 2.18 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 OD2 ASP B 80 CD CD A 105 3555 1.63 REMARK 500 O HOH B 156 O HOH B 199 3555 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP B 80 CB - CG - OD2 ANGL. DEV. = 9.4 DEGREES 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 GLU A 16 -44.34 -149.82 REMARK 500 ASP A 85 146.27 -170.30 REMARK 500 GLU B 16 -36.75 -135.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET B 70 14.62 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 B 179 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH A 154 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH A 155 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH A 192 DISTANCE = 6.79 ANGSTROMS
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 FE A 108 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 0 NE2 REMARK 620 2 GLU B 41 OE2 97.0 REMARK 620 3 HOH A 189 O 91.8 91.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 105 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 40 OE1 REMARK 620 2 GLU A 40 OE2 54.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 106 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 80 OD1 REMARK 620 2 ASP A 80 OD2 53.0 REMARK 620 3 HOH A 109 O 98.4 107.6 REMARK 620 4 HOH A 191 O 145.9 95.5 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 107 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 104 O REMARK 620 2 LEU A 104 OXT 51.8 REMARK 620 3 HOH A 187 O 79.4 84.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 106 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 41 OE2 REMARK 620 2 HOH B 202 O 86.7 REMARK 620 3 HOH B 149 O 80.9 158.8 REMARK 620 4 HOH B 201 O 72.6 78.8 81.1 REMARK 620 5 HOH B 203 O 98.4 89.0 109.7 165.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 105 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 47 OE1 REMARK 620 2 GLU B 47 OE2 55.8 REMARK 620 3 HOH B 198 O 102.5 103.8 REMARK 620 N 1 2
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 105 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 106 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 107 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 108 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 105 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 106
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O7K RELATED DB: PDB REMARK 900 NON MUTATED PROTEIN REMARK 900 RELATED ID: 2O89 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, P31T/C32S MUTANT REMARK 900 RELATED ID: 2O87 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, P31S MUTANT REMARK 900 RELATED ID: 2O85 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, P31T MUTANT
DBREF 3DIE A 1 104 UNP P0A0K6 THIO_STAAU 1 104 DBREF 3DIE B 1 104 UNP P0A0K6 THIO_STAAU 1 104
SEQADV 3DIE SER A -1 UNP P0A0K6 EXPRESSION TAG SEQADV 3DIE HIS A 0 UNP P0A0K6 EXPRESSION TAG SEQADV 3DIE ALA A 28 UNP P0A0K6 TRP 28 ENGINEERED SEQADV 3DIE SER B -1 UNP P0A0K6 EXPRESSION TAG SEQADV 3DIE HIS B 0 UNP P0A0K6 EXPRESSION TAG SEQADV 3DIE ALA B 28 UNP P0A0K6 TRP 28 ENGINEERED
SEQRES 1 A 106 SER HIS MET ALA ILE VAL LYS VAL THR ASP ALA ASP PHE SEQRES 2 A 106 ASP SER LYS VAL GLU SER GLY VAL GLN LEU VAL ASP PHE SEQRES 3 A 106 TRP ALA THR ALA CYS GLY PRO CYS LYS MET ILE ALA PRO SEQRES 4 A 106 VAL LEU GLU GLU LEU ALA ALA ASP TYR GLU GLY LYS ALA SEQRES 5 A 106 ASP ILE LEU LYS LEU ASP VAL ASP GLU ASN PRO SER THR SEQRES 6 A 106 ALA ALA LYS TYR GLU VAL MET SER ILE PRO THR LEU ILE SEQRES 7 A 106 VAL PHE LYS ASP GLY GLN PRO VAL ASP LYS VAL VAL GLY SEQRES 8 A 106 PHE GLN PRO LYS GLU ASN LEU ALA GLU VAL LEU ASP LYS SEQRES 9 A 106 HIS LEU SEQRES 1 B 106 SER HIS MET ALA ILE VAL LYS VAL THR ASP ALA ASP PHE SEQRES 2 B 106 ASP SER LYS VAL GLU SER GLY VAL GLN LEU VAL ASP PHE SEQRES 3 B 106 TRP ALA THR ALA CYS GLY PRO CYS LYS MET ILE ALA PRO SEQRES 4 B 106 VAL LEU GLU GLU LEU ALA ALA ASP TYR GLU GLY LYS ALA SEQRES 5 B 106 ASP ILE LEU LYS LEU ASP VAL ASP GLU ASN PRO SER THR SEQRES 6 B 106 ALA ALA LYS TYR GLU VAL MET SER ILE PRO THR LEU ILE SEQRES 7 B 106 VAL PHE LYS ASP GLY GLN PRO VAL ASP LYS VAL VAL GLY SEQRES 8 B 106 PHE GLN PRO LYS GLU ASN LEU ALA GLU VAL LEU ASP LYS SEQRES 9 B 106 HIS LEU
HET CD A 105 1 HET CD A 106 1 HET CD A 107 1 HET FE A 108 1 HET CD B 105 1 HET FE B 106 1
HETNAM CD CADMIUM ION HETNAM FE FE (III) ION
FORMUL 3 CD 4(CD 2+) FORMUL 6 FE 2(FE 3+) FORMUL 9 HOH *141(H2 O)
HELIX 1 1 ASP A 10 VAL A 15 1 6 HELIX 2 2 CYS A 29 TYR A 46 1 18 HELIX 3 3 ASN A 60 TYR A 67 1 8 HELIX 4 4 PRO A 92 LYS A 102 1 11 HELIX 5 5 ASP B 10 VAL B 15 1 6 HELIX 6 6 CYS B 29 TYR B 46 1 18 HELIX 7 7 ASN B 60 TYR B 67 1 8 HELIX 8 8 PRO B 92 LYS B 102 1 11
SHEET 1 A 5 VAL A 4 LYS A 5 0 SHEET 2 A 5 ALA B 50 ASP B 56 1 O LYS B 54 N VAL A 4 SHEET 3 A 5 VAL A 19 TRP A 25 1 N LEU A 21 O LEU B 53 SHEET 4 A 5 THR B 74 LYS B 79 -1 O PHE B 78 N GLN A 20 SHEET 5 A 5 GLN B 82 VAL B 88 -1 O VAL B 84 N VAL B 77 SHEET 1 B 5 GLN A 82 VAL A 88 0 SHEET 2 B 5 THR A 74 LYS A 79 -1 N VAL A 77 O ASP A 85 SHEET 3 B 5 VAL B 19 TRP B 25 -1 O GLN B 20 N PHE A 78 SHEET 4 B 5 ASP A 51 ASP A 56 1 N LEU A 53 O LEU B 21 SHEET 5 B 5 VAL B 4 LYS B 5 1 O VAL B 4 N LYS A 54
SSBOND 1 CYS A 29 CYS A 32 1555 1555 2.05 SSBOND 2 CYS B 29 CYS B 32 1555 1555 2.03
LINK NE2 HIS A 0 FE FE A 108 1555 1555 2.35 LINK OE1 GLU A 40 CD CD A 105 1555 1555 2.31 LINK OE2 GLU A 40 CD CD A 105 1555 1555 2.43 LINK OD1 ASP A 80 CD CD A 106 1555 1555 2.58 LINK OD2 ASP A 80 CD CD A 106 1555 1555 2.24 LINK O LEU A 104 CD CD A 107 1555 1555 2.44 LINK OXT LEU A 104 CD CD A 107 1555 1555 2.40 LINK OE2 GLU B 41 FE FE A 108 1555 1555 2.36 LINK OE2 GLU B 41 FE FE B 106 1555 1555 2.42 LINK OE1 GLU B 47 CD CD B 105 1555 1555 2.51 LINK OE2 GLU B 47 CD CD B 105 1555 1555 2.13 LINK CD CD A 106 O HOH A 109 1555 1555 2.51 LINK CD CD A 106 O HOH A 191 1555 1555 2.44 LINK CD CD A 107 O HOH A 187 1555 1555 2.19 LINK FE FE A 108 O HOH A 189 1555 1555 2.24 LINK CD CD B 105 O HOH B 198 1555 1555 1.99 LINK FE FE B 106 O HOH B 202 1555 1555 1.73 LINK FE FE B 106 O HOH B 149 1555 1555 2.44 LINK FE FE B 106 O HOH B 201 1555 1555 2.06 LINK FE FE B 106 O HOH B 203 1555 1555 2.13
CISPEP 1 ILE A 72 PRO A 73 0 1.85 CISPEP 2 ILE B 72 PRO B 73 0 -3.78
SITE 1 AC1 4 GLU A 40 ASP B 80 HOH B 154 HOH B 164 SITE 1 AC2 4 ASP A 80 HOH A 109 HOH A 191 GLU B 40 SITE 1 AC3 5 ALA A 9 ASP A 12 LEU A 104 HOH A 187 SITE 2 AC3 5 HOH A 188 SITE 1 AC4 6 HIS A 0 HOH A 162 HOH A 176 HOH A 189 SITE 2 AC4 6 GLU B 41 HOH B 149 SITE 1 AC5 2 GLU B 47 HOH B 198 SITE 1 AC6 6 GLU A 16 GLU B 41 HOH B 149 HOH B 201 SITE 2 AC6 6 HOH B 202 HOH B 203
CRYST1 88.703 84.451 34.699 90.00 90.00 90.00 P 21 21 2 8
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 0.011274 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011841 0.000000 0.00000
SCALE3 0.000000 0.000000 0.028819 0.00000