HEADER TRANSFERASE 24-APR-09 3H7F TITLE CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SERINE METHYLASE 1, SHMT 1; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: 1719B; SOURCE 5 GENE: GLYA1, GLYA, RV1093, MT1125, MTV017.46; 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: AVA0421 KEYWDS MYCOBACTERIUM TUBERCULOSIS, SERINE HYDROXYMETHYLTRANSFERASE, ONE- KEYWDS 2 CARBON METABOLISM, PYRIDOXAL PHOSPHATE, TRANSFERASE, STRUCTURAL KEYWDS 3 GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, KEYWDS 4 SSGCID EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 22-NOV-23 3H7F 1 REMARK REVDAT 3 06-SEP-23 3H7F 1 REMARK SEQADV LINK REVDAT 2 22-APR-15 3H7F 1 JRNL VERSN REVDAT 1 05-MAY-09 3H7F 0 JRNL AUTH L.BAUGH,I.PHAN,D.W.BEGLEY,M.C.CLIFTON,B.ARMOUR,D.M.DRANOW, JRNL AUTH 2 B.M.TAYLOR,M.M.MURUTHI,J.ABENDROTH,J.W.FAIRMAN,D.FOX, JRNL AUTH 3 S.H.DIETERICH,B.L.STAKER,A.S.GARDBERG,R.CHOI,S.N.HEWITT, JRNL AUTH 4 A.J.NAPULI,J.MYERS,L.K.BARRETT,Y.ZHANG,M.FERRELL,E.MUNDT, JRNL AUTH 5 K.THOMPKINS,N.TRAN,S.LYONS-ABBOTT,A.ABRAMOV,A.SEKAR, JRNL AUTH 6 D.SERBZHINSKIY,D.LORIMER,G.W.BUCHKO,R.STACY,L.J.STEWART, JRNL AUTH 7 T.E.EDWARDS,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL INCREASING THE STRUCTURAL COVERAGE OF TUBERCULOSIS DRUG JRNL TITL 2 TARGETS. JRNL REF TUBERCULOSIS (EDINB) V. 95 142 2015 JRNL REFN ISSN 1472-9792 JRNL PMID 25613812 JRNL DOI 10.1016/J.TUBE.2014.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 130877 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6606 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9007 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 498 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 962 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -1.12000 REMARK 3 B33 (A**2) : 1.17000 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): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.361 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6536 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4326 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8932 ; 1.629 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10584 ; 1.168 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 897 ; 5.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 271 ;35.072 ;23.469 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;12.112 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;15.580 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1027 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7507 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1312 ; 0.001 ; 0.020 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): 4253 ; 0.803 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1756 ; 0.245 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6793 ; 1.334 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2283 ; 2.177 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2111 ; 3.421 ; 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 : 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 : 1.40 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 4 REMARK 4 3H7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 130938 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 80.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: PDB ENTRY 2DKJ MODIFIED BY CCP4 PROGRAM CHAINSAW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HAMPTON INDEX, G12: 25% PEG 3350, REMARK 280 200MM MGCL2, 100MM HEPES, MYTUD.00783.A AT 20 MG/ML, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K 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 30.36500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.36500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.00500 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: 9330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 MET A -20 REMARK 465 ALA A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 MET A -12 REMARK 465 GLY A -11 REMARK 465 THR A -10 REMARK 465 LEU A -9 REMARK 465 GLU A -8 REMARK 465 ALA A -7 REMARK 465 GLN A -6 REMARK 465 THR A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 ASN A 347 REMARK 465 ALA A 348 REMARK 465 VAL A 349 REMARK 465 PRO A 350 REMARK 465 ASN A 351 REMARK 465 ASP A 352 REMARK 465 PRO A 353 REMARK 465 ARG A 354 REMARK 465 PRO A 355 REMARK 465 PRO A 356 REMARK 465 MET A 357 REMARK 465 VAL A 358 REMARK 465 THR A 359 REMARK 465 ARG A 426 REMARK 465 MET B -20 REMARK 465 ALA B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 MET B -12 REMARK 465 GLY B -11 REMARK 465 THR B -10 REMARK 465 LEU B -9 REMARK 465 GLU B -8 REMARK 465 ALA B -7 REMARK 465 GLN B -6 REMARK 465 THR B -5 REMARK 465 GLN B -4 REMARK 465 GLY B -3 REMARK 465 PRO B -2 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 ARG A 59 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 291 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 SER A 394 OG REMARK 470 SER A 395 OG REMARK 470 ARG A 407 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 420 CG CD OE1 OE2 REMARK 470 ARG B 129 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 426 CG CD NE CZ NH1 NH2 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 OD1 ASP B 117 O HOH B 951 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 OG SER A 360 O HOH A 731 3555 2.01 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 LLP A 227 -141.46 71.30 REMARK 500 SER A 311 -1.18 77.44 REMARK 500 VAL A 316 -161.63 -124.60 REMARK 500 ALA B 53 42.62 -144.46 REMARK 500 ARG B 59 56.86 -143.69 REMARK 500 LLP B 227 -145.91 74.98 REMARK 500 SER B 234 172.07 176.69 REMARK 500 THR B 359 169.48 68.31 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 MG B 427 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 567 O REMARK 620 2 HOH B 582 O 92.8 REMARK 620 3 HOH B 643 O 175.3 82.8 REMARK 620 4 HOH B 748 O 89.2 177.4 95.2 REMARK 620 5 HOH B 980 O 98.2 88.8 83.3 92.8 REMARK 620 6 HOH B 981 O 88.3 91.5 90.2 86.7 173.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 427 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MYTUD.00783.A RELATED DB: TARGETDB DBREF 3H7F A 1 426 UNP O53441 GLYA1_MYCTU 1 426 DBREF 3H7F B 1 426 UNP O53441 GLYA1_MYCTU 1 426 SEQADV 3H7F MET A -20 UNP O53441 EXPRESSION TAG SEQADV 3H7F ALA A -19 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -18 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -17 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -16 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -15 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -14 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS A -13 UNP O53441 EXPRESSION TAG SEQADV 3H7F MET A -12 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY A -11 UNP O53441 EXPRESSION TAG SEQADV 3H7F THR A -10 UNP O53441 EXPRESSION TAG SEQADV 3H7F LEU A -9 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLU A -8 UNP O53441 EXPRESSION TAG SEQADV 3H7F ALA A -7 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLN A -6 UNP O53441 EXPRESSION TAG SEQADV 3H7F THR A -5 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLN A -4 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY A -3 UNP O53441 EXPRESSION TAG SEQADV 3H7F PRO A -2 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY A -1 UNP O53441 EXPRESSION TAG SEQADV 3H7F SER A 0 UNP O53441 EXPRESSION TAG SEQADV 3H7F MET B -20 UNP O53441 EXPRESSION TAG SEQADV 3H7F ALA B -19 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -18 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -17 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -16 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -15 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -14 UNP O53441 EXPRESSION TAG SEQADV 3H7F HIS B -13 UNP O53441 EXPRESSION TAG SEQADV 3H7F MET B -12 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY B -11 UNP O53441 EXPRESSION TAG SEQADV 3H7F THR B -10 UNP O53441 EXPRESSION TAG SEQADV 3H7F LEU B -9 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLU B -8 UNP O53441 EXPRESSION TAG SEQADV 3H7F ALA B -7 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLN B -6 UNP O53441 EXPRESSION TAG SEQADV 3H7F THR B -5 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLN B -4 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY B -3 UNP O53441 EXPRESSION TAG SEQADV 3H7F PRO B -2 UNP O53441 EXPRESSION TAG SEQADV 3H7F GLY B -1 UNP O53441 EXPRESSION TAG SEQADV 3H7F SER B 0 UNP O53441 EXPRESSION TAG SEQRES 1 A 447 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 A 447 ALA GLN THR GLN GLY PRO GLY SER MET SER ALA PRO LEU SEQRES 3 A 447 ALA GLU VAL ASP PRO ASP ILE ALA GLU LEU LEU ALA LYS SEQRES 4 A 447 GLU LEU GLY ARG GLN ARG ASP THR LEU GLU MET ILE ALA SEQRES 5 A 447 SER GLU ASN PHE VAL PRO ARG ALA VAL LEU GLN ALA GLN SEQRES 6 A 447 GLY SER VAL LEU THR ASN LYS TYR ALA GLU GLY LEU PRO SEQRES 7 A 447 GLY ARG ARG TYR TYR GLY GLY CYS GLU HIS VAL ASP VAL SEQRES 8 A 447 VAL GLU ASN LEU ALA ARG ASP ARG ALA LYS ALA LEU PHE SEQRES 9 A 447 GLY ALA GLU PHE ALA ASN VAL GLN PRO HIS SER GLY ALA SEQRES 10 A 447 GLN ALA ASN ALA ALA VAL LEU HIS ALA LEU MET SER PRO SEQRES 11 A 447 GLY GLU ARG LEU LEU GLY LEU ASP LEU ALA ASN GLY GLY SEQRES 12 A 447 HIS LEU THR HIS GLY MET ARG LEU ASN PHE SER GLY LYS SEQRES 13 A 447 LEU TYR GLU ASN GLY PHE TYR GLY VAL ASP PRO ALA THR SEQRES 14 A 447 HIS LEU ILE ASP MET ASP ALA VAL ARG ALA THR ALA LEU SEQRES 15 A 447 GLU PHE ARG PRO LYS VAL ILE ILE ALA GLY TRP SER ALA SEQRES 16 A 447 TYR PRO ARG VAL LEU ASP PHE ALA ALA PHE ARG SER ILE SEQRES 17 A 447 ALA ASP GLU VAL GLY ALA LYS LEU LEU VAL ASP MET ALA SEQRES 18 A 447 HIS PHE ALA GLY LEU VAL ALA ALA GLY LEU HIS PRO SER SEQRES 19 A 447 PRO VAL PRO HIS ALA ASP VAL VAL SER THR THR VAL HIS SEQRES 20 A 447 LLP THR LEU GLY GLY GLY ARG SER GLY LEU ILE VAL GLY SEQRES 21 A 447 LYS GLN GLN TYR ALA LYS ALA ILE ASN SER ALA VAL PHE SEQRES 22 A 447 PRO GLY GLN GLN GLY GLY PRO LEU MET HIS VAL ILE ALA SEQRES 23 A 447 GLY LYS ALA VAL ALA LEU LYS ILE ALA ALA THR PRO GLU SEQRES 24 A 447 PHE ALA ASP ARG GLN ARG ARG THR LEU SER GLY ALA ARG SEQRES 25 A 447 ILE ILE ALA ASP ARG LEU MET ALA PRO ASP VAL ALA LYS SEQRES 26 A 447 ALA GLY VAL SER VAL VAL SER GLY GLY THR ASP VAL HIS SEQRES 27 A 447 LEU VAL LEU VAL ASP LEU ARG ASP SER PRO LEU ASP GLY SEQRES 28 A 447 GLN ALA ALA GLU ASP LEU LEU HIS GLU VAL GLY ILE THR SEQRES 29 A 447 VAL ASN ARG ASN ALA VAL PRO ASN ASP PRO ARG PRO PRO SEQRES 30 A 447 MET VAL THR SER GLY LEU ARG ILE GLY THR PRO ALA LEU SEQRES 31 A 447 ALA THR ARG GLY PHE GLY ASP THR GLU PHE THR GLU VAL SEQRES 32 A 447 ALA ASP ILE ILE ALA THR ALA LEU ALA THR GLY SER SER SEQRES 33 A 447 VAL ASP VAL SER ALA LEU LYS ASP ARG ALA THR ARG LEU SEQRES 34 A 447 ALA ARG ALA PHE PRO LEU TYR ASP GLY LEU GLU GLU TRP SEQRES 35 A 447 SER LEU VAL GLY ARG SEQRES 1 B 447 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 B 447 ALA GLN THR GLN GLY PRO GLY SER MET SER ALA PRO LEU SEQRES 3 B 447 ALA GLU VAL ASP PRO ASP ILE ALA GLU LEU LEU ALA LYS SEQRES 4 B 447 GLU LEU GLY ARG GLN ARG ASP THR LEU GLU MET ILE ALA SEQRES 5 B 447 SER GLU ASN PHE VAL PRO ARG ALA VAL LEU GLN ALA GLN SEQRES 6 B 447 GLY SER VAL LEU THR ASN LYS TYR ALA GLU GLY LEU PRO SEQRES 7 B 447 GLY ARG ARG TYR TYR GLY GLY CYS GLU HIS VAL ASP VAL SEQRES 8 B 447 VAL GLU ASN LEU ALA ARG ASP ARG ALA LYS ALA LEU PHE SEQRES 9 B 447 GLY ALA GLU PHE ALA ASN VAL GLN PRO HIS SER GLY ALA SEQRES 10 B 447 GLN ALA ASN ALA ALA VAL LEU HIS ALA LEU MET SER PRO SEQRES 11 B 447 GLY GLU ARG LEU LEU GLY LEU ASP LEU ALA ASN GLY GLY SEQRES 12 B 447 HIS LEU THR HIS GLY MET ARG LEU ASN PHE SER GLY LYS SEQRES 13 B 447 LEU TYR GLU ASN GLY PHE TYR GLY VAL ASP PRO ALA THR SEQRES 14 B 447 HIS LEU ILE ASP MET ASP ALA VAL ARG ALA THR ALA LEU SEQRES 15 B 447 GLU PHE ARG PRO LYS VAL ILE ILE ALA GLY TRP SER ALA SEQRES 16 B 447 TYR PRO ARG VAL LEU ASP PHE ALA ALA PHE ARG SER ILE SEQRES 17 B 447 ALA ASP GLU VAL GLY ALA LYS LEU LEU VAL ASP MET ALA SEQRES 18 B 447 HIS PHE ALA GLY LEU VAL ALA ALA GLY LEU HIS PRO SER SEQRES 19 B 447 PRO VAL PRO HIS ALA ASP VAL VAL SER THR THR VAL HIS SEQRES 20 B 447 LLP THR LEU GLY GLY GLY ARG SER GLY LEU ILE VAL GLY SEQRES 21 B 447 LYS GLN GLN TYR ALA LYS ALA ILE ASN SER ALA VAL PHE SEQRES 22 B 447 PRO GLY GLN GLN GLY GLY PRO LEU MET HIS VAL ILE ALA SEQRES 23 B 447 GLY LYS ALA VAL ALA LEU LYS ILE ALA ALA THR PRO GLU SEQRES 24 B 447 PHE ALA ASP ARG GLN ARG ARG THR LEU SER GLY ALA ARG SEQRES 25 B 447 ILE ILE ALA ASP ARG LEU MET ALA PRO ASP VAL ALA LYS SEQRES 26 B 447 ALA GLY VAL SER VAL VAL SER GLY GLY THR ASP VAL HIS SEQRES 27 B 447 LEU VAL LEU VAL ASP LEU ARG ASP SER PRO LEU ASP GLY SEQRES 28 B 447 GLN ALA ALA GLU ASP LEU LEU HIS GLU VAL GLY ILE THR SEQRES 29 B 447 VAL ASN ARG ASN ALA VAL PRO ASN ASP PRO ARG PRO PRO SEQRES 30 B 447 MET VAL THR SER GLY LEU ARG ILE GLY THR PRO ALA LEU SEQRES 31 B 447 ALA THR ARG GLY PHE GLY ASP THR GLU PHE THR GLU VAL SEQRES 32 B 447 ALA ASP ILE ILE ALA THR ALA LEU ALA THR GLY SER SER SEQRES 33 B 447 VAL ASP VAL SER ALA LEU LYS ASP ARG ALA THR ARG LEU SEQRES 34 B 447 ALA ARG ALA PHE PRO LEU TYR ASP GLY LEU GLU GLU TRP SEQRES 35 B 447 SER LEU VAL GLY ARG MODRES 3H7F LLP A 227 LYS MODRES 3H7F LLP B 227 LYS HET LLP A 227 24 HET LLP B 227 24 HET MG B 427 1 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM MG MAGNESIUM ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 MG MG 2+ FORMUL 4 HOH *962(H2 O) HELIX 1 1 GLY A -1 ALA A 3 5 5 HELIX 2 2 PRO A 4 ASP A 9 1 6 HELIX 3 3 ASP A 9 THR A 26 1 18 HELIX 4 4 PRO A 37 GLY A 45 1 9 HELIX 5 5 SER A 46 LYS A 51 5 6 HELIX 6 6 CYS A 65 GLY A 84 1 20 HELIX 7 7 SER A 94 MET A 107 1 14 HELIX 8 8 LEU A 118 GLY A 121 5 4 HELIX 9 9 HIS A 123 GLY A 127 5 5 HELIX 10 10 ASN A 131 LEU A 136 1 6 HELIX 11 11 ASP A 152 ARG A 164 1 13 HELIX 12 12 ASP A 180 GLY A 192 1 13 HELIX 13 13 PHE A 202 ALA A 208 1 7 HELIX 14 14 HIS A 226 GLY A 230 5 5 HELIX 15 15 TYR A 243 PHE A 252 1 10 HELIX 16 16 LEU A 260 ALA A 274 1 15 HELIX 17 17 THR A 276 MET A 298 1 23 HELIX 18 18 ALA A 299 ALA A 305 1 7 HELIX 19 19 SER A 311 GLY A 313 5 3 HELIX 20 20 ASP A 329 VAL A 340 1 12 HELIX 21 21 THR A 366 GLY A 373 1 8 HELIX 22 22 GLY A 375 THR A 392 1 18 HELIX 23 23 GLY A 393 VAL A 396 5 4 HELIX 24 24 ASP A 397 PHE A 412 1 16 HELIX 25 25 GLY A 417 TRP A 421 5 5 HELIX 26 26 GLY B -1 ALA B 3 5 5 HELIX 27 27 PRO B 4 ASP B 9 1 6 HELIX 28 28 ASP B 9 THR B 26 1 18 HELIX 29 29 PRO B 37 GLY B 45 1 9 HELIX 30 30 SER B 46 LYS B 51 5 6 HELIX 31 31 CYS B 65 GLY B 84 1 20 HELIX 32 32 SER B 94 MET B 107 1 14 HELIX 33 33 LEU B 118 GLY B 121 5 4 HELIX 34 34 HIS B 123 GLY B 127 5 5 HELIX 35 35 ASN B 131 LEU B 136 1 6 HELIX 36 36 ASP B 152 ARG B 164 1 13 HELIX 37 37 ASP B 180 GLY B 192 1 13 HELIX 38 38 PHE B 202 ALA B 208 1 7 HELIX 39 39 HIS B 226 GLY B 230 5 5 HELIX 40 40 TYR B 243 PHE B 252 1 10 HELIX 41 41 LEU B 260 ALA B 275 1 16 HELIX 42 42 THR B 276 MET B 298 1 23 HELIX 43 43 ALA B 299 ALA B 305 1 7 HELIX 44 44 SER B 311 GLY B 313 5 3 HELIX 45 45 ASP B 329 VAL B 340 1 12 HELIX 46 46 THR B 366 GLY B 373 1 8 HELIX 47 47 GLY B 375 THR B 392 1 18 HELIX 48 48 GLY B 393 VAL B 396 5 4 HELIX 49 49 ASP B 397 PHE B 412 1 16 HELIX 50 50 GLY B 417 TRP B 421 5 5 SHEET 1 A 2 LEU A 27 GLU A 28 0 SHEET 2 A 2 ILE A 342 THR A 343 1 O THR A 343 N LEU A 27 SHEET 1 B 2 GLY A 55 LEU A 56 0 SHEET 2 B 2 ARG A 59 ARG A 60 -1 O ARG A 59 N LEU A 56 SHEET 1 C 7 PHE A 87 ASN A 89 0 SHEET 2 C 7 GLY A 235 GLY A 239 -1 O ILE A 237 N ASN A 89 SHEET 3 C 7 VAL A 220 THR A 224 -1 N VAL A 221 O VAL A 238 SHEET 4 C 7 LYS A 194 ASP A 198 1 N VAL A 197 O SER A 222 SHEET 5 C 7 VAL A 167 GLY A 171 1 N ILE A 168 O LYS A 194 SHEET 6 C 7 ARG A 112 LEU A 116 1 N LEU A 114 O ILE A 169 SHEET 7 C 7 GLU A 138 TYR A 142 1 O GLY A 140 N LEU A 113 SHEET 1 D 3 SER A 308 VAL A 309 0 SHEET 2 D 3 LEU A 318 ASP A 322 -1 O ASP A 322 N SER A 308 SHEET 3 D 3 GLY A 361 GLY A 365 -1 O LEU A 362 N VAL A 321 SHEET 1 E 2 LEU B 27 GLU B 28 0 SHEET 2 E 2 ILE B 342 THR B 343 1 O THR B 343 N LEU B 27 SHEET 1 F 2 GLY B 55 LEU B 56 0 SHEET 2 F 2 ARG B 59 ARG B 60 -1 O ARG B 59 N LEU B 56 SHEET 1 G 7 PHE B 87 ASN B 89 0 SHEET 2 G 7 GLY B 235 GLY B 239 -1 O ILE B 237 N ASN B 89 SHEET 3 G 7 VAL B 220 THR B 224 -1 N VAL B 221 O VAL B 238 SHEET 4 G 7 LYS B 194 ASP B 198 1 N VAL B 197 O VAL B 220 SHEET 5 G 7 VAL B 167 GLY B 171 1 N ILE B 168 O LYS B 194 SHEET 6 G 7 ARG B 112 LEU B 116 1 N LEU B 114 O ILE B 169 SHEET 7 G 7 GLU B 138 TYR B 142 1 O GLU B 138 N LEU B 113 SHEET 1 H 4 SER B 308 VAL B 309 0 SHEET 2 H 4 LEU B 318 ASP B 322 -1 O ASP B 322 N SER B 308 SHEET 3 H 4 GLY B 361 GLY B 365 -1 O LEU B 362 N VAL B 321 SHEET 4 H 4 ASN B 345 ARG B 346 -1 N ASN B 345 O ARG B 363 LINK C HIS A 226 N LLP A 227 1555 1555 1.31 LINK C LLP A 227 N THR A 228 1555 1555 1.33 LINK C HIS B 226 N LLP B 227 1555 1555 1.33 LINK C LLP B 227 N THR B 228 1555 1555 1.33 LINK MG MG B 427 O HOH B 567 1555 1555 2.05 LINK MG MG B 427 O HOH B 582 1555 1555 2.03 LINK MG MG B 427 O HOH B 643 1555 1555 2.20 LINK MG MG B 427 O HOH B 748 1555 1555 2.14 LINK MG MG B 427 O HOH B 980 1555 1555 1.99 LINK MG MG B 427 O HOH B 981 1555 1555 2.07 CISPEP 1 PHE A 252 PRO A 253 0 3.89 CISPEP 2 PHE B 252 PRO B 253 0 8.56 SITE 1 AC1 6 HOH B 567 HOH B 582 HOH B 643 HOH B 748 SITE 2 AC1 6 HOH B 980 HOH B 981 CRYST1 60.730 102.010 132.120 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 0.016466 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007569 0.00000