10 20 30 40 50 60 70 80 3DKI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 25-JUN-08 3DKI
TITLE 2.1 A X-RAY STRUCTURE OF CYSM (RV1336) FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS AN O-PHOSPHOSERINE DEPENDENT CYSTEINE SYNTHASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE SYNTHASE B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: O-ACETYLSERINE SULFHYDRYLASE B, CSASE B, O- COMPND 5 ACETYLSERINE (THIOL)-LYASE B, CYSM; COMPND 6 EC: 2.5.1.65; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: CYSM, RV1336; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS CYSTEINE SYNTHASE, O-PHOSPHOSERINE, CYSO(RV1335), PYRIDOXAL- KEYWDS 2 PHOSPHATE, PLP, AMINO-ACID BIOSYNTHESIS, CYSTEINE KEYWDS 3 BIOSYNTHESIS, PYRIDOXAL PHOSPHATE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.AGREN,R.SCHNELL,G.SCHNEIDER
REVDAT 3 24-FEB-09 3DKI 1 VERSN REVDAT 2 25-NOV-08 3DKI 1 JRNL REVDAT 1 16-SEP-08 3DKI 0
JRNL AUTH D.AGREN,R.SCHNELL,W.OEHLMANN,M.SINGH,G.SCHNEIDER JRNL TITL CYSTEINE SYNTHASE (CYSM) OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS IS AN O-PHOSPHOSERINE SULFHYDRYLASE: JRNL TITL 3 EVIDENCE FOR AN ALTERNATIVE CYSTEINE BIOSYNTHESIS JRNL TITL 4 PATHWAY IN MYCOBACTERIA JRNL REF J.BIOL.CHEM. V. 283 31567 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18799456 JRNL DOI 10.1074/JBC.M804877200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 36490 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) : 0.191 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1898 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.27000 REMARK 3 B22 (A**2) : -1.10000 REMARK 3 B33 (A**2) : 0.82000 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): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.198 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4653 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3073 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6338 ; 1.398 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7460 ; 0.957 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 602 ; 5.851 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;31.112 ;22.953 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 714 ;15.845 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;14.248 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 720 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5267 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 939 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 992 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3281 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2269 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2499 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.189 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.086 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.268 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.280 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.315 ; 0.200 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): 2991 ; 0.682 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1245 ; 0.138 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4757 ; 1.275 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1727 ; 2.029 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1581 ; 3.236 ; 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 : BABINET MODEL WITH 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 ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3DKI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB048151.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93400 REMARK 200 MONOCHROMATOR : CHANNEL CUT ESRF MONOCHROMATOR REMARK 200 OPTICS : CHANNEL CUT ESRF REMARK 200 MONOCHROMATOR, TORODIAL REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38431 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45300 REMARK 200 R SYM FOR SHELL (I) : 0.53900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2Q3B REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 7.5, 0.1M K2HPO4, REMARK 280 4.3M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 37.21150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.38300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.61100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.38300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.21150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.61100 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: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 314 REMARK 465 THR A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 GLY A 319 REMARK 465 GLN A 320 REMARK 465 LEU A 321 REMARK 465 TRP A 322 REMARK 465 ALA A 323 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 ALA B 125 REMARK 465 GLU B 126 REMARK 465 GLY B 127 REMARK 465 GLY B 128 REMARK 465 SER B 129 REMARK 465 ASN B 130 REMARK 465 ARG B 211 REMARK 465 TYR B 212 REMARK 465 GLY B 213 REMARK 465 GLU B 214 REMARK 465 GLY B 215 REMARK 465 VAL B 216 REMARK 465 TYR B 217 REMARK 465 ALA B 218 REMARK 465 LEU B 219 REMARK 465 ARG B 220 REMARK 465 ASN B 221 REMARK 465 MET B 222 REMARK 465 ASP B 223 REMARK 465 GLU B 224 REMARK 465 GLY B 225 REMARK 465 PHE B 226 REMARK 465 LEU B 317 REMARK 465 GLU B 318 REMARK 465 GLY B 319 REMARK 465 GLN B 320 REMARK 465 LEU B 321 REMARK 465 TRP B 322 REMARK 465 ALA B 323
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 TYR B 300 OG1 THR B 303 2.13 REMARK 500 O GLU B 229 O HOH B 350 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 328 O HOH A 407 4545 2.17 REMARK 500 OD2 ASP A 28 O HOH A 328 4445 2.18 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 10 48.50 -90.86 REMARK 500 ASN A 104 -7.56 -54.26 REMARK 500 TYR A 150 78.24 57.53 REMARK 500 THR A 186 -2.95 83.15 REMARK 500 ALA A 218 -9.50 78.61 REMARK 500 SER A 302 3.13 -65.25 REMARK 500 ALA B 2 45.70 -144.52 REMARK 500 ALA B 10 33.28 -96.63 REMARK 500 PRO B 70 -58.81 -23.12 REMARK 500 ASN B 104 37.64 -98.40 REMARK 500 TYR B 150 78.18 67.62 REMARK 500 SER B 302 58.12 -64.53 REMARK 500 THR B 303 -176.65 -170.87 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 367 DISTANCE = 5.23 ANGSTROMS REMARK 525 HOH B 370 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH B 374 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH B 392 DISTANCE = 5.31 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 NA B 324 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 140 O REMARK 620 2 ASN B 143 O 82.3 REMARK 620 3 TRP B 146 O 95.1 87.4 REMARK 620 4 HOH B 376 O 84.3 165.6 99.3 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 NA B 324
DBREF 3DKI A 1 323 UNP P63873 CYSM_MYCTU 1 323 DBREF 3DKI B 1 323 UNP P63873 CYSM_MYCTU 1 323
SEQADV 3DKI GLY A -2 UNP P63873 EXPRESSION TAG SEQADV 3DKI SER A -1 UNP P63873 EXPRESSION TAG SEQADV 3DKI HIS A 0 UNP P63873 EXPRESSION TAG SEQADV 3DKI ALA A 2 UNP P63873 THR 2 ENGINEERED SEQADV 3DKI GLY B -2 UNP P63873 EXPRESSION TAG SEQADV 3DKI SER B -1 UNP P63873 EXPRESSION TAG SEQADV 3DKI HIS B 0 UNP P63873 EXPRESSION TAG SEQADV 3DKI ALA B 2 UNP P63873 THR 2 ENGINEERED
SEQRES 1 A 326 GLY SER HIS MET ALA ARG TYR ASP SER LEU LEU GLN ALA SEQRES 2 A 326 LEU GLY ASN THR PRO LEU VAL GLY LEU GLN ARG LEU SER SEQRES 3 A 326 PRO ARG TRP ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG SEQRES 4 A 326 LEU TRP ALA LYS LEU GLU ASP ARG ASN PRO THR GLY SER SEQRES 5 A 326 ILE LLP ASP ARG PRO ALA VAL ARG MET ILE GLU GLN ALA SEQRES 6 A 326 GLU ALA ASP GLY LEU LEU ARG PRO GLY ALA THR ILE LEU SEQRES 7 A 326 GLU PRO THR SER GLY ASN THR GLY ILE SER LEU ALA MET SEQRES 8 A 326 ALA ALA ARG LEU LYS GLY TYR ARG LEU ILE CYS VAL MET SEQRES 9 A 326 PRO GLU ASN THR SER VAL GLU ARG ARG GLN LEU LEU GLU SEQRES 10 A 326 LEU TYR GLY ALA GLN ILE ILE PHE SER ALA ALA GLU GLY SEQRES 11 A 326 GLY SER ASN THR ALA VAL ALA THR ALA LYS GLU LEU ALA SEQRES 12 A 326 ALA THR ASN PRO SER TRP VAL MET LEU TYR GLN TYR GLY SEQRES 13 A 326 ASN PRO ALA ASN THR ASP SER HIS TYR CYS GLY THR GLY SEQRES 14 A 326 PRO GLU LEU LEU ALA ASP LEU PRO GLU ILE THR HIS PHE SEQRES 15 A 326 VAL ALA GLY LEU GLY THR THR GLY THR LEU MET GLY THR SEQRES 16 A 326 GLY ARG PHE LEU ARG GLU HIS VAL ALA ASN VAL LYS ILE SEQRES 17 A 326 VAL ALA ALA GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA SEQRES 18 A 326 LEU ARG ASN MET ASP GLU GLY PHE VAL PRO GLU LEU TYR SEQRES 19 A 326 ASP PRO GLU ILE LEU THR ALA ARG TYR SER VAL GLY ALA SEQRES 20 A 326 VAL ASP ALA VAL ARG ARG THR ARG GLU LEU VAL HIS THR SEQRES 21 A 326 GLU GLY ILE PHE ALA GLY ILE SER THR GLY ALA VAL LEU SEQRES 22 A 326 HIS ALA ALA LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA SEQRES 23 A 326 GLY GLU ARG ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA SEQRES 24 A 326 GLY TRP LYS TYR LEU SER THR GLY ALA TYR ALA GLY SER SEQRES 25 A 326 LEU ASP ASP ALA GLU THR ALA LEU GLU GLY GLN LEU TRP SEQRES 26 A 326 ALA SEQRES 1 B 326 GLY SER HIS MET ALA ARG TYR ASP SER LEU LEU GLN ALA SEQRES 2 B 326 LEU GLY ASN THR PRO LEU VAL GLY LEU GLN ARG LEU SER SEQRES 3 B 326 PRO ARG TRP ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG SEQRES 4 B 326 LEU TRP ALA LYS LEU GLU ASP ARG ASN PRO THR GLY SER SEQRES 5 B 326 ILE LLP ASP ARG PRO ALA VAL ARG MET ILE GLU GLN ALA SEQRES 6 B 326 GLU ALA ASP GLY LEU LEU ARG PRO GLY ALA THR ILE LEU SEQRES 7 B 326 GLU PRO THR SER GLY ASN THR GLY ILE SER LEU ALA MET SEQRES 8 B 326 ALA ALA ARG LEU LYS GLY TYR ARG LEU ILE CYS VAL MET SEQRES 9 B 326 PRO GLU ASN THR SER VAL GLU ARG ARG GLN LEU LEU GLU SEQRES 10 B 326 LEU TYR GLY ALA GLN ILE ILE PHE SER ALA ALA GLU GLY SEQRES 11 B 326 GLY SER ASN THR ALA VAL ALA THR ALA LYS GLU LEU ALA SEQRES 12 B 326 ALA THR ASN PRO SER TRP VAL MET LEU TYR GLN TYR GLY SEQRES 13 B 326 ASN PRO ALA ASN THR ASP SER HIS TYR CYS GLY THR GLY SEQRES 14 B 326 PRO GLU LEU LEU ALA ASP LEU PRO GLU ILE THR HIS PHE SEQRES 15 B 326 VAL ALA GLY LEU GLY THR THR GLY THR LEU MET GLY THR SEQRES 16 B 326 GLY ARG PHE LEU ARG GLU HIS VAL ALA ASN VAL LYS ILE SEQRES 17 B 326 VAL ALA ALA GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA SEQRES 18 B 326 LEU ARG ASN MET ASP GLU GLY PHE VAL PRO GLU LEU TYR SEQRES 19 B 326 ASP PRO GLU ILE LEU THR ALA ARG TYR SER VAL GLY ALA SEQRES 20 B 326 VAL ASP ALA VAL ARG ARG THR ARG GLU LEU VAL HIS THR SEQRES 21 B 326 GLU GLY ILE PHE ALA GLY ILE SER THR GLY ALA VAL LEU SEQRES 22 B 326 HIS ALA ALA LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA SEQRES 23 B 326 GLY GLU ARG ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA SEQRES 24 B 326 GLY TRP LYS TYR LEU SER THR GLY ALA TYR ALA GLY SER SEQRES 25 B 326 LEU ASP ASP ALA GLU THR ALA LEU GLU GLY GLN LEU TRP SEQRES 26 B 326 ALA
MODRES 3DKI LLP A 51 LYS MODRES 3DKI LLP B 51 LYS
HET LLP A 51 24 HET LLP B 51 24 HET NA B 324 1
HETNAM LLP 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- HETNAM 2 LLP PYRIDIN-4-YLMETHANE) HETNAM NA SODIUM ION
HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
FORMUL 1 LLP 2(C14 H24 N3 O7 P) FORMUL 3 NA NA 1+ FORMUL 4 HOH *219(H2 O)
HELIX 1 1 SER A 6 ALA A 10 5 5 HELIX 2 2 ASP A 43 ASN A 45 5 3 HELIX 3 3 LLP A 51 ASP A 65 1 15 HELIX 4 4 GLY A 80 LYS A 93 1 14 HELIX 5 5 SER A 106 TYR A 116 1 11 HELIX 6 6 GLY A 127 ALA A 141 1 15 HELIX 7 7 ASN A 154 GLY A 164 1 11 HELIX 8 8 GLY A 164 LEU A 173 1 10 HELIX 9 9 THR A 186 VAL A 200 1 15 HELIX 10 10 ASP A 232 LEU A 236 5 5 HELIX 11 11 GLY A 243 GLY A 259 1 17 HELIX 12 12 GLY A 263 GLY A 284 1 22 HELIX 13 13 GLY A 297 GLY A 304 5 8 HELIX 14 14 SER B 6 LEU B 11 5 6 HELIX 15 15 ASP B 43 ASN B 45 5 3 HELIX 16 16 LLP B 51 ASP B 65 1 15 HELIX 17 17 GLY B 80 GLY B 94 1 15 HELIX 18 18 SER B 106 TYR B 116 1 11 HELIX 19 19 THR B 131 ALA B 141 1 11 HELIX 20 20 ASN B 154 GLY B 164 1 11 HELIX 21 21 GLY B 164 LEU B 173 1 10 HELIX 22 22 THR B 186 GLU B 198 1 13 HELIX 23 23 GLY B 243 GLY B 259 1 17 HELIX 24 24 GLY B 263 ALA B 283 1 21 HELIX 25 25 GLY B 297 LEU B 301 5 5 HELIX 26 26 SER B 309 ALA B 316 1 8
SHEET 1 A 7 ALA A 238 VAL A 242 0 SHEET 2 A 7 LYS A 204 PRO A 210 1 N ALA A 207 O ALA A 238 SHEET 3 A 7 HIS A 178 GLY A 182 1 N PHE A 179 O VAL A 206 SHEET 4 A 7 ALA A 287 VAL A 293 1 O ALA A 290 N VAL A 180 SHEET 5 A 7 VAL A 35 LEU A 41 1 N ARG A 36 O ILE A 289 SHEET 6 A 7 LEU A 16 GLY A 18 -1 N VAL A 17 O ALA A 39 SHEET 7 A 7 ARG B 3 TYR B 4 1 O TYR B 4 N LEU A 16 SHEET 1 B 4 GLN A 119 SER A 123 0 SHEET 2 B 4 ARG A 96 PRO A 102 1 N CYS A 99 O GLN A 119 SHEET 3 B 4 THR A 73 GLU A 76 1 N ILE A 74 O ARG A 96 SHEET 4 B 4 TRP A 146 MET A 148 1 O VAL A 147 N THR A 73 SHEET 1 C 6 LEU B 16 GLY B 18 0 SHEET 2 C 6 VAL B 35 LEU B 41 -1 O ALA B 39 N VAL B 17 SHEET 3 C 6 ALA B 287 VAL B 293 1 O LEU B 291 N LYS B 40 SHEET 4 C 6 HIS B 178 GLY B 182 1 N VAL B 180 O ALA B 290 SHEET 5 C 6 LYS B 204 GLU B 209 1 O VAL B 206 N PHE B 179 SHEET 6 C 6 ALA B 238 SER B 241 1 O TYR B 240 N GLU B 209 SHEET 1 D 4 GLN B 119 SER B 123 0 SHEET 2 D 4 ARG B 96 PRO B 102 1 N CYS B 99 O GLN B 119 SHEET 3 D 4 THR B 73 PRO B 77 1 N ILE B 74 O ARG B 96 SHEET 4 D 4 TRP B 146 MET B 148 1 O VAL B 147 N LEU B 75
LINK C ILE A 50 N LLP A 51 1555 1555 1.33 LINK C LLP A 51 N ASP A 52 1555 1555 1.32 LINK C ILE B 50 N LLP B 51 1555 1555 1.33 LINK C LLP B 51 N ASP B 52 1555 1555 1.33 LINK O ALA B 140 NA NA B 324 1555 1555 2.28 LINK O ASN B 143 NA NA B 324 1555 1555 2.37 LINK O TRP B 146 NA NA B 324 1555 1555 2.33 LINK NA NA B 324 O HOH B 376 1555 1555 2.35
SITE 1 AC1 4 ALA B 140 ASN B 143 TRP B 146 HOH B 376
CRYST1 74.423 89.222 98.766 90.00 90.00 90.00 P 21 21 21 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 0.013437 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011208 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010125 0.00000