HEADER TRANSFERASE 05-OCT-15 5E40 TITLE 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS WITH D-TYROSINE BOUND IN THE PHENYLALANINE TITLE 3 BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.5.1.54; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: AROG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINO ACID, ALLOSTERIC REGULATION, SHIKIMATE PATHWAY, 3-DEOXY-D- KEYWDS 2 ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.REICHAU,W.JIAO,E.J.PARKER REVDAT 2 27-SEP-23 5E40 1 REMARK LINK REVDAT 1 01-JUN-16 5E40 0 JRNL AUTH S.REICHAU,N.J.BLACKMORE,W.JIAO,E.J.PARKER JRNL TITL PROBING THE SOPHISTICATED SYNERGISTIC ALLOSTERIC REGULATION JRNL TITL 2 OF AROMATIC AMINO ACID BIOSYNTHESIS IN MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS USING -AMINO ACIDS. JRNL REF PLOS ONE V. 11 52723 2016 JRNL REFN ESSN 1932-6203 JRNL PMID 27128682 JRNL DOI 10.1371/JOURNAL.PONE.0152723 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 96017 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5046 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7036 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 404 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7045 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 537 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.44000 REMARK 3 B22 (A**2) : 2.44000 REMARK 3 B33 (A**2) : -4.88000 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): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7324 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6953 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9981 ; 1.155 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15939 ; 0.806 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 933 ; 5.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 343 ;34.373 ;23.411 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1168 ;12.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 70 ;15.924 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1126 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8427 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1687 ; 0.004 ; 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): 3702 ; 1.279 ; 2.669 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3701 ; 1.279 ; 2.669 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4627 ; 2.339 ; 3.994 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5E40 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : SILICON DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101083 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 19.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 1.02600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 3NV8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 7.5, 1.5 M AMMONIUM REMARK 280 SULFATE, 12% V/V GLYCEROL. FOR SOAKING, 0.2 MICROLITERS OF A 10 REMARK 280 MM D-TYR STOCK SOLUTION WAS ADDED TO EQUILIBRATED 2 MICROLITER REMARK 280 DROPLETS AT 48 HOURS AND 24 HOURS BEFORE CRYSTAL FREEZING, REMARK 280 RESPECTIVELY, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.53533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.26767 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.26767 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.53533 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 64070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -277.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -22.26767 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 633 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 618 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 ALA A 0 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 465 ASP B 10 REMARK 465 GLN B 11 REMARK 465 LEU B 12 REMARK 465 PRO B 13 REMARK 465 SER B 14 REMARK 465 LEU B 15 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 11 CG CD OE1 NE2 REMARK 470 LEU A 12 CG CD1 CD2 REMARK 470 ASP A 235 CG OD1 OD2 REMARK 470 GLN A 239 CG CD OE1 NE2 REMARK 470 ASP B 235 CG OD1 OD2 REMARK 470 ARG B 236 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 239 CG CD OE1 NE2 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 CYS A 440 -107.87 -149.24 REMARK 500 ASP B 235 0.49 86.05 REMARK 500 CYS B 440 -108.03 -149.47 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 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 87 SG REMARK 620 2 HIS A 369 NE2 176.9 REMARK 620 3 GLU A 411 OE1 97.4 85.7 REMARK 620 4 GLU A 411 OE2 96.0 86.0 53.9 REMARK 620 5 ASP A 441 OD2 92.0 87.4 96.4 149.9 REMARK 620 6 HOH A 724 O 96.7 80.6 153.9 102.8 105.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 87 SG REMARK 620 2 HIS B 369 NE2 175.7 REMARK 620 3 GLU B 411 OE1 97.3 87.1 REMARK 620 4 GLU B 411 OE2 94.5 87.7 54.3 REMARK 620 5 ASP B 441 OD2 93.2 86.7 98.1 152.0 REMARK 620 6 HOH B 760 O 94.1 81.8 153.6 101.2 105.1 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTY A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTY B 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NV8 RELATED DB: PDB REMARK 900 3NV8 CONTAINS THE SAME PROTEIN IN COMPLEX WITH ONLY THE SUBSTRATE REMARK 900 PEP, IN THE ABSENCE OF ALLOSTERIC LIGANDS. REMARK 900 RELATED ID: 2YPP RELATED DB: PDB REMARK 900 2YPP CONTAINS THE SAME PROTEIN WITH L-TYROSINE BOUND IN THE REMARK 900 TYROSINE AND PHENYLALANINE BINDING SITES. REMARK 900 RELATED ID: 5E2L RELATED DB: PDB REMARK 900 5E2L CONTAINS THE SAME PROTEIN WITH D-PHENYLALANINE BOUND IN THE REMARK 900 PHENYLALANINE BINDING SITE. REMARK 900 RELATED ID: 3KGF RELATED DB: PDB REMARK 900 3KGF CONTAINS THE SAME PROTEIN WITH L-TRYPTOPHAN BOUND IN THE REMARK 900 TRYPTOPHAN BINDING SITE AND L-PHENYLALANINE BOUND IN THE REMARK 900 PHENYLALANINE AND TYROSINE SITES. REMARK 900 RELATED ID: 3NUD RELATED DB: PDB REMARK 900 3NUD CONTAINS THE SAME PROTEIN WITH L-PHENYLALANINE BOUND IN ALL REMARK 900 THREE ALLOSTERIC SITES. REMARK 900 RELATED ID: 3NUE RELATED DB: PDB REMARK 900 3NUE CONTAINS THE SAME PROTEIN WITH L-TRYPTOPHAN BOUND IN THE REMARK 900 TRYPTOPHAN BINDING SITE. REMARK 900 RELATED ID: 3RZI RELATED DB: PDB REMARK 900 3RZI CONTAINS THE SAME PROTEIN CO-CRYSTALLIZED WITH L-TRYPTOPHAN REMARK 900 (BOUND IN THE TRP BINDING SITE) AND L-PHENYLALANINE (BOUND IN THE REMARK 900 PHE BINDING SITE). REMARK 900 RELATED ID: 2YPO RELATED DB: PDB REMARK 900 2YPO CONTAINS THE SAME PROTEIN WITH L-PHENYLALANINE BOUND ONLY IN REMARK 900 THE PHENYLALANINE BINDING SITE. REMARK 900 RELATED ID: 2YPQ RELATED DB: PDB REMARK 900 2YPQ CONTAINS THE SAME PROTEIN WITH L-TRYPTOPHAN BOUND IN THE REMARK 900 TRYPTOPHAN BINDING SITE AND L-TYROSINE BOUND IN THE TYROSINE AND REMARK 900 PHENYLALANINE BINDING SITES. REMARK 900 RELATED ID: 5E4N RELATED DB: PDB DBREF1 5E40 A 1 462 UNP A0A0E8NFD1_MYCTX DBREF2 5E40 A A0A0E8NFD1 1 462 DBREF1 5E40 B 1 462 UNP A0A0E8NFD1_MYCTX DBREF2 5E40 B A0A0E8NFD1 1 462 SEQADV 5E40 GLY A -1 UNP A0A0E8NFD EXPRESSION TAG SEQADV 5E40 ALA A 0 UNP A0A0E8NFD EXPRESSION TAG SEQADV 5E40 GLY B -1 UNP A0A0E8NFD EXPRESSION TAG SEQADV 5E40 ALA B 0 UNP A0A0E8NFD EXPRESSION TAG SEQRES 1 A 464 GLY ALA MET ASN TRP THR VAL ASP ILE PRO ILE ASP GLN SEQRES 2 A 464 LEU PRO SER LEU PRO PRO LEU PRO THR ASP LEU ARG THR SEQRES 3 A 464 ARG LEU ASP ALA ALA LEU ALA LYS PRO ALA ALA GLN GLN SEQRES 4 A 464 PRO THR TRP PRO ALA ASP GLN ALA LEU ALA MET ARG THR SEQRES 5 A 464 VAL LEU GLU SER VAL PRO PRO VAL THR VAL PRO SER GLU SEQRES 6 A 464 ILE VAL ARG LEU GLN GLU GLN LEU ALA GLN VAL ALA LYS SEQRES 7 A 464 GLY GLU ALA PHE LEU LEU GLN GLY GLY ASP CYS ALA GLU SEQRES 8 A 464 THR PHE MET ASP ASN THR GLU PRO HIS ILE ARG GLY ASN SEQRES 9 A 464 VAL ARG ALA LEU LEU GLN MET ALA VAL VAL LEU THR TYR SEQRES 10 A 464 GLY ALA SER MET PRO VAL VAL LYS VAL ALA ARG ILE ALA SEQRES 11 A 464 GLY GLN TYR ALA LYS PRO ARG SER ALA ASP ILE ASP ALA SEQRES 12 A 464 LEU GLY LEU ARG SER TYR ARG GLY ASP MET ILE ASN GLY SEQRES 13 A 464 PHE ALA PRO ASP ALA ALA ALA ARG GLU HIS ASP PRO SER SEQRES 14 A 464 ARG LEU VAL ARG ALA TYR ALA ASN ALA SER ALA ALA MET SEQRES 15 A 464 ASN LEU VAL ARG ALA LEU THR SER SER GLY LEU ALA SER SEQRES 16 A 464 LEU HIS LEU VAL HIS ASP TRP ASN ARG GLU PHE VAL ARG SEQRES 17 A 464 THR SER PRO ALA GLY ALA ARG TYR GLU ALA LEU ALA THR SEQRES 18 A 464 GLU ILE ASP ARG GLY LEU ARG PHE MET SER ALA CYS GLY SEQRES 19 A 464 VAL ALA ASP ARG ASN LEU GLN THR ALA GLU ILE TYR ALA SEQRES 20 A 464 SER HIS GLU ALA LEU VAL LEU ASP TYR GLU ARG ALA MET SEQRES 21 A 464 LEU ARG LEU SER ASP GLY ASP ASP GLY GLU PRO GLN LEU SEQRES 22 A 464 PHE ASP LEU SER ALA HIS THR VAL TRP ILE GLY GLU ARG SEQRES 23 A 464 THR ARG GLN ILE ASP GLY ALA HIS ILE ALA PHE ALA GLN SEQRES 24 A 464 VAL ILE ALA ASN PRO VAL GLY VAL LYS LEU GLY PRO ASN SEQRES 25 A 464 MET THR PRO GLU LEU ALA VAL GLU TYR VAL GLU ARG LEU SEQRES 26 A 464 ASP PRO HIS ASN LYS PRO GLY ARG LEU THR LEU VAL SER SEQRES 27 A 464 ARG MET GLY ASN HIS LYS VAL ARG ASP LEU LEU PRO PRO SEQRES 28 A 464 ILE VAL GLU LYS VAL GLN ALA THR GLY HIS GLN VAL ILE SEQRES 29 A 464 TRP GLN CYS ASP PRO MET HIS GLY ASN THR HIS GLU SER SEQRES 30 A 464 SER THR GLY PHE LYS THR ARG HIS PHE ASP ARG ILE VAL SEQRES 31 A 464 ASP GLU VAL GLN GLY PHE PHE GLU VAL HIS ARG ALA LEU SEQRES 32 A 464 GLY THR HIS PRO GLY GLY ILE HIS VAL GLU ILE THR GLY SEQRES 33 A 464 GLU ASN VAL THR GLU CYS LEU GLY GLY ALA GLN ASP ILE SEQRES 34 A 464 SER GLU THR ASP LEU ALA GLY ARG TYR GLU THR ALA CYS SEQRES 35 A 464 ASP PRO ARG LEU ASN THR GLN GLN SER LEU GLU LEU ALA SEQRES 36 A 464 PHE LEU VAL ALA GLU MET LEU ARG ASP SEQRES 1 B 464 GLY ALA MET ASN TRP THR VAL ASP ILE PRO ILE ASP GLN SEQRES 2 B 464 LEU PRO SER LEU PRO PRO LEU PRO THR ASP LEU ARG THR SEQRES 3 B 464 ARG LEU ASP ALA ALA LEU ALA LYS PRO ALA ALA GLN GLN SEQRES 4 B 464 PRO THR TRP PRO ALA ASP GLN ALA LEU ALA MET ARG THR SEQRES 5 B 464 VAL LEU GLU SER VAL PRO PRO VAL THR VAL PRO SER GLU SEQRES 6 B 464 ILE VAL ARG LEU GLN GLU GLN LEU ALA GLN VAL ALA LYS SEQRES 7 B 464 GLY GLU ALA PHE LEU LEU GLN GLY GLY ASP CYS ALA GLU SEQRES 8 B 464 THR PHE MET ASP ASN THR GLU PRO HIS ILE ARG GLY ASN SEQRES 9 B 464 VAL ARG ALA LEU LEU GLN MET ALA VAL VAL LEU THR TYR SEQRES 10 B 464 GLY ALA SER MET PRO VAL VAL LYS VAL ALA ARG ILE ALA SEQRES 11 B 464 GLY GLN TYR ALA LYS PRO ARG SER ALA ASP ILE ASP ALA SEQRES 12 B 464 LEU GLY LEU ARG SER TYR ARG GLY ASP MET ILE ASN GLY SEQRES 13 B 464 PHE ALA PRO ASP ALA ALA ALA ARG GLU HIS ASP PRO SER SEQRES 14 B 464 ARG LEU VAL ARG ALA TYR ALA ASN ALA SER ALA ALA MET SEQRES 15 B 464 ASN LEU VAL ARG ALA LEU THR SER SER GLY LEU ALA SER SEQRES 16 B 464 LEU HIS LEU VAL HIS ASP TRP ASN ARG GLU PHE VAL ARG SEQRES 17 B 464 THR SER PRO ALA GLY ALA ARG TYR GLU ALA LEU ALA THR SEQRES 18 B 464 GLU ILE ASP ARG GLY LEU ARG PHE MET SER ALA CYS GLY SEQRES 19 B 464 VAL ALA ASP ARG ASN LEU GLN THR ALA GLU ILE TYR ALA SEQRES 20 B 464 SER HIS GLU ALA LEU VAL LEU ASP TYR GLU ARG ALA MET SEQRES 21 B 464 LEU ARG LEU SER ASP GLY ASP ASP GLY GLU PRO GLN LEU SEQRES 22 B 464 PHE ASP LEU SER ALA HIS THR VAL TRP ILE GLY GLU ARG SEQRES 23 B 464 THR ARG GLN ILE ASP GLY ALA HIS ILE ALA PHE ALA GLN SEQRES 24 B 464 VAL ILE ALA ASN PRO VAL GLY VAL LYS LEU GLY PRO ASN SEQRES 25 B 464 MET THR PRO GLU LEU ALA VAL GLU TYR VAL GLU ARG LEU SEQRES 26 B 464 ASP PRO HIS ASN LYS PRO GLY ARG LEU THR LEU VAL SER SEQRES 27 B 464 ARG MET GLY ASN HIS LYS VAL ARG ASP LEU LEU PRO PRO SEQRES 28 B 464 ILE VAL GLU LYS VAL GLN ALA THR GLY HIS GLN VAL ILE SEQRES 29 B 464 TRP GLN CYS ASP PRO MET HIS GLY ASN THR HIS GLU SER SEQRES 30 B 464 SER THR GLY PHE LYS THR ARG HIS PHE ASP ARG ILE VAL SEQRES 31 B 464 ASP GLU VAL GLN GLY PHE PHE GLU VAL HIS ARG ALA LEU SEQRES 32 B 464 GLY THR HIS PRO GLY GLY ILE HIS VAL GLU ILE THR GLY SEQRES 33 B 464 GLU ASN VAL THR GLU CYS LEU GLY GLY ALA GLN ASP ILE SEQRES 34 B 464 SER GLU THR ASP LEU ALA GLY ARG TYR GLU THR ALA CYS SEQRES 35 B 464 ASP PRO ARG LEU ASN THR GLN GLN SER LEU GLU LEU ALA SEQRES 36 B 464 PHE LEU VAL ALA GLU MET LEU ARG ASP HET SO4 A 501 5 HET MN A 502 1 HET DTY A 503 13 HET SO4 B 501 5 HET SO4 B 502 5 HET SO4 B 503 5 HET SO4 B 504 5 HET GOL B 505 6 HET MN B 506 1 HET DTY B 507 13 HETNAM SO4 SULFATE ION HETNAM MN MANGANESE (II) ION HETNAM DTY D-TYROSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 5(O4 S 2-) FORMUL 4 MN 2(MN 2+) FORMUL 5 DTY 2(C9 H11 N O3) FORMUL 10 GOL C3 H8 O3 FORMUL 13 HOH *537(H2 O) HELIX 1 AA1 PRO A 19 ALA A 31 1 13 HELIX 2 AA2 PRO A 41 SER A 54 1 14 HELIX 3 AA3 VAL A 60 LYS A 76 1 17 HELIX 4 AA4 THR A 95 SER A 118 1 24 HELIX 5 AA5 ASP A 158 GLU A 163 1 6 HELIX 6 AA6 SER A 167 SER A 188 1 22 HELIX 7 AA7 SER A 189 ALA A 192 5 4 HELIX 8 AA8 SER A 193 SER A 208 1 16 HELIX 9 AA9 ALA A 210 CYS A 231 1 22 HELIX 10 AB1 ASP A 235 THR A 240 1 6 HELIX 11 AB2 VAL A 251 MET A 258 1 8 HELIX 12 AB3 GLY A 290 ILE A 299 1 10 HELIX 13 AB4 THR A 312 ASP A 324 1 13 HELIX 14 AB5 LYS A 342 ALA A 356 1 15 HELIX 15 AB6 HIS A 383 GLY A 402 1 20 HELIX 16 AB7 THR A 430 GLY A 434 5 5 HELIX 17 AB8 ASN A 445 ASP A 462 1 18 HELIX 18 AB9 PRO B 19 LYS B 32 1 14 HELIX 19 AC1 PRO B 41 SER B 54 1 14 HELIX 20 AC2 VAL B 60 LYS B 76 1 17 HELIX 21 AC3 THR B 95 SER B 118 1 24 HELIX 22 AC4 ASP B 158 GLU B 163 1 6 HELIX 23 AC5 SER B 167 SER B 189 1 23 HELIX 24 AC6 GLY B 190 ALA B 192 5 3 HELIX 25 AC7 SER B 193 THR B 207 1 15 HELIX 26 AC8 ALA B 210 CYS B 231 1 22 HELIX 27 AC9 VAL B 251 MET B 258 1 8 HELIX 28 AD1 GLY B 290 ILE B 299 1 10 HELIX 29 AD2 THR B 312 ASP B 324 1 13 HELIX 30 AD3 LYS B 342 ALA B 356 1 15 HELIX 31 AD4 HIS B 383 GLY B 402 1 20 HELIX 32 AD5 THR B 430 GLY B 434 5 5 HELIX 33 AD6 ASN B 445 ASP B 462 1 18 SHEET 1 AA1 2 THR A 4 PRO A 8 0 SHEET 2 AA1 2 ASN B 2 ASP B 6 -1 O TRP B 3 N ILE A 7 SHEET 1 AA2 9 PHE A 80 GLY A 85 0 SHEET 2 AA2 9 VAL A 121 ARG A 126 1 O VAL A 122 N LEU A 82 SHEET 3 AA2 9 ILE A 243 GLU A 248 1 O TYR A 244 N ALA A 125 SHEET 4 AA2 9 THR A 278 ILE A 281 1 N THR A 278 O ALA A 245 SHEET 5 AA2 9 VAL A 303 LEU A 307 1 O GLY A 304 N ILE A 281 SHEET 6 AA2 9 LEU A 332 SER A 336 1 O VAL A 335 N LEU A 307 SHEET 7 AA2 9 ILE A 362 CYS A 365 1 O ILE A 362 N LEU A 334 SHEET 8 AA2 9 GLY A 407 GLU A 411 1 O GLY A 407 N CYS A 365 SHEET 9 AA2 9 PHE A 80 GLY A 85 1 N GLN A 83 O VAL A 410 SHEET 1 AA3 2 LEU A 259 LEU A 261 0 SHEET 2 AA3 2 LEU A 271 ASP A 273 -1 O PHE A 272 N ARG A 260 SHEET 1 AA4 2 THR A 372 GLU A 374 0 SHEET 2 AA4 2 LYS A 380 ARG A 382 -1 O THR A 381 N HIS A 373 SHEET 1 AA5 9 PHE B 80 GLY B 85 0 SHEET 2 AA5 9 VAL B 121 ARG B 126 1 O VAL B 122 N LEU B 82 SHEET 3 AA5 9 ILE B 243 GLU B 248 1 O TYR B 244 N ALA B 125 SHEET 4 AA5 9 THR B 278 ILE B 281 1 N THR B 278 O ALA B 245 SHEET 5 AA5 9 VAL B 303 LEU B 307 1 O GLY B 304 N ILE B 281 SHEET 6 AA5 9 LEU B 332 SER B 336 1 O VAL B 335 N LEU B 307 SHEET 7 AA5 9 ILE B 362 CYS B 365 1 O ILE B 362 N LEU B 334 SHEET 8 AA5 9 GLY B 407 GLU B 411 1 O GLY B 407 N CYS B 365 SHEET 9 AA5 9 PHE B 80 GLY B 85 1 N GLN B 83 O VAL B 410 SHEET 1 AA6 2 LEU B 259 LEU B 261 0 SHEET 2 AA6 2 LEU B 271 ASP B 273 -1 O PHE B 272 N ARG B 260 SHEET 1 AA7 2 THR B 372 GLU B 374 0 SHEET 2 AA7 2 LYS B 380 ARG B 382 -1 O THR B 381 N HIS B 373 LINK SG CYS A 87 MN MN A 502 1555 1555 2.52 LINK NE2 HIS A 369 MN MN A 502 1555 1555 2.35 LINK OE1 GLU A 411 MN MN A 502 1555 1555 2.63 LINK OE2 GLU A 411 MN MN A 502 1555 1555 2.13 LINK OD2 ASP A 441 MN MN A 502 1555 1555 2.32 LINK MN MN A 502 O HOH A 724 1555 1555 2.01 LINK SG CYS B 87 MN MN B 506 1555 1555 2.55 LINK NE2 HIS B 369 MN MN B 506 1555 1555 2.35 LINK OE1 GLU B 411 MN MN B 506 1555 1555 2.60 LINK OE2 GLU B 411 MN MN B 506 1555 1555 2.15 LINK OD2 ASP B 441 MN MN B 506 1555 1555 2.26 LINK MN MN B 506 O HOH B 760 1555 1555 1.96 SITE 1 AC1 10 GLY A 282 GLU A 283 LYS A 306 ARG A 337 SITE 2 AC1 10 HIS A 369 HOH A 614 HOH A 663 HOH A 708 SITE 3 AC1 10 HOH A 723 HOH A 744 SITE 1 AC2 5 CYS A 87 HIS A 369 GLU A 411 ASP A 441 SITE 2 AC2 5 HOH A 724 SITE 1 AC3 10 PHE A 91 ARG A 171 ALA A 174 ASN A 175 SITE 2 AC3 10 HOH A 624 HOH A 648 VAL B 55 TYR B 173 SITE 3 AC3 10 ALA B 174 HOH B 661 SITE 1 AC4 8 GLY B 282 GLU B 283 LYS B 306 ARG B 337 SITE 2 AC4 8 HOH B 611 HOH B 655 HOH B 758 HOH B 759 SITE 1 AC5 9 PRO B 17 LEU B 18 ARG B 23 LEU B 144 SITE 2 AC5 9 ASP B 158 ALA B 159 HOH B 635 HOH B 780 SITE 3 AC5 9 HOH B 808 SITE 1 AC6 5 ARG B 135 SER B 136 ALA B 137 ARG B 284 SITE 2 AC6 5 HOH B 761 SITE 1 AC7 8 ARG B 23 LEU B 26 ARG B 256 HOH B 656 SITE 2 AC7 8 HOH B 674 HOH B 722 HOH B 807 HOH B 819 SITE 1 AC8 6 GLU B 63 MET B 180 THR B 187 ILE B 243 SITE 2 AC8 6 HOH B 605 HOH B 709 SITE 1 AC9 5 CYS B 87 HIS B 369 GLU B 411 ASP B 441 SITE 2 AC9 5 HOH B 760 SITE 1 AD1 9 ASP A 10 TYR A 173 ALA A 174 PHE B 91 SITE 2 AD1 9 ARG B 171 ALA B 174 ASN B 175 HOH B 621 SITE 3 AD1 9 HOH B 727 CRYST1 205.451 205.451 66.803 90.00 90.00 120.00 P 32 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.004867 0.002810 0.000000 0.00000 SCALE2 0.000000 0.005620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014969 0.00000