HEADER TRANSFERASE 01-OCT-12 4HCQ TITLE CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX TITLE 2 WITH GLUCOSAMINE-1-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PROTEIN GLMU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE, N- COMPND 5 ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, GLUCOSAMINE-1- COMPND 6 PHOSPHATE N-ACETYLTRANSFERASE; COMPND 7 EC: 2.7.7.23, 2.3.1.157; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: GLMU, RV1018C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQEII KEYWDS ACETYLTRANSFERASE, BIFUNCTIONAL, PYROPHOSPHORYLASE, ROSSMANN-LIKE KEYWDS 2 FOLD, LEFT-HANDED-BETA-HELIX, CELL SHAPE, CELL WALL KEYWDS 3 BIOGENESIS/DEGRADATION, MAGNESIUM, METAL-BINDING, MULTIFUNCTIONAL KEYWDS 4 ENZYME, NUCLEOTIDYLTRANSFERASE, PEPTIDOGLYCAN SYNTHESIS, KEYWDS 5 TRANSFERASE, ACYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.K.A.JAGTAP,S.K.VERMA,N.VITHANI REVDAT 5 08-NOV-23 4HCQ 1 HETSYN REVDAT 4 29-JUL-20 4HCQ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 20-NOV-19 4HCQ 1 SEQADV LINK REVDAT 2 10-JUL-13 4HCQ 1 JRNL REVDAT 1 13-MAR-13 4HCQ 0 JRNL AUTH P.K.A.JAGTAP,S.K.VERMA,N.VITHANI,V.S.BAIS,B.PRAKASH JRNL TITL CRYSTAL STRUCTURES IDENTIFY AN ATYPICAL TWO-METAL-ION JRNL TITL 2 MECHANISM FOR URIDYLTRANSFER IN GLMU: ITS SIGNIFICANCE TO JRNL TITL 3 SUGAR NUCLEOTIDYL TRANSFERASES JRNL REF J.MOL.BIOL. V. 425 1745 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23485416 JRNL DOI 10.1016/J.JMB.2013.02.019 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19855 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1011 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1343 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3309 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.309 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3397 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4648 ; 1.979 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 7.226 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;36.034 ;23.459 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 508 ;18.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;24.951 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 579 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2538 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2231 ; 0.928 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3597 ; 1.730 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1166 ; 2.634 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1051 ; 4.326 ; 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 : 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 RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4HCQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19893 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.932 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3DJ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 150MM NACL, 5% GLYCEROL, REMARK 280 1,3-BUTANEDIOL, AMPPNP, MGCL2, 0.1M HEPES, COCL2, DTT, PH 7.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.63500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.88328 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.24333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 39.63500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.88328 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 92.24333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 39.63500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.88328 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.24333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.76656 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 184.48667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.76656 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 184.48667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.76656 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 184.48667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -267.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 PHE A 3 REMARK 465 PRO A 4 REMARK 465 GLY A 5 REMARK 465 TYR A 398 REMARK 465 ASP A 399 REMARK 465 GLY A 400 REMARK 465 THR A 401 REMARK 465 SER A 402 REMARK 465 LYS A 403 REMARK 465 ARG A 404 REMARK 465 ARG A 465 REMARK 465 PRO A 466 REMARK 465 GLY A 467 REMARK 465 SER A 468 REMARK 465 PRO A 469 REMARK 465 ALA A 470 REMARK 465 ALA A 471 REMARK 465 GLN A 472 REMARK 465 ALA A 473 REMARK 465 SER A 474 REMARK 465 LYS A 475 REMARK 465 ARG A 476 REMARK 465 ALA A 477 REMARK 465 SER A 478 REMARK 465 GLU A 479 REMARK 465 MET A 480 REMARK 465 ALA A 481 REMARK 465 CYS A 482 REMARK 465 GLN A 483 REMARK 465 GLN A 484 REMARK 465 PRO A 485 REMARK 465 THR A 486 REMARK 465 GLN A 487 REMARK 465 PRO A 488 REMARK 465 PRO A 489 REMARK 465 ASP A 490 REMARK 465 ALA A 491 REMARK 465 ASP A 492 REMARK 465 GLN A 493 REMARK 465 THR A 494 REMARK 465 PRO A 495 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 604 O HOH A 605 1.58 REMARK 500 OP1 GN1 A 502 O HOH A 605 1.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 160 CG GLU A 160 CD 0.094 REMARK 500 GLY A 305 N GLY A 305 CA 0.126 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 LEU A 247 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 253 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 283 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 301 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 GLY A 305 N - CA - C ANGL. DEV. = -17.7 DEGREES REMARK 500 PRO A 306 C - N - CA ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG A 405 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 405 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 413 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ARG A 21 67.26 37.52 REMARK 500 ALA A 32 19.20 57.13 REMARK 500 ASP A 59 14.06 81.72 REMARK 500 PRO A 86 68.63 -59.43 REMARK 500 THR A 156 -174.12 -65.04 REMARK 500 ARG A 295 40.91 -105.44 REMARK 500 PHE A 340 61.83 68.39 REMARK 500 ALA A 351 144.55 -37.79 REMARK 500 ASP A 352 16.49 55.63 REMARK 500 SER A 450 -18.41 -151.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 304 GLY A 305 -124.18 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 A 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 114 OD2 REMARK 620 2 ASN A 239 OD1 95.1 REMARK 620 3 HOH A 602 O 93.7 121.5 REMARK 620 4 HOH A 604 O 112.3 145.8 78.3 REMARK 620 5 HOH A 605 O 107.2 116.0 116.1 37.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 503 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 417 OD1 REMARK 620 2 ASP A 417 OD2 59.7 REMARK 620 3 ASP A 417 OD1 0.0 59.7 REMARK 620 4 ASP A 417 OD2 59.7 0.0 59.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 417 OD1 REMARK 620 2 ASP A 417 OD1 0.0 REMARK 620 3 HOH A 687 O 103.2 103.2 REMARK 620 4 HOH A 687 O 94.0 94.0 85.1 REMARK 620 N 1 2 3 DBREF 4HCQ A 1 495 UNP P96382 GLMU_MYCTU 1 495 SEQADV 4HCQ HIS A -5 UNP P96382 EXPRESSION TAG SEQADV 4HCQ HIS A -4 UNP P96382 EXPRESSION TAG SEQADV 4HCQ HIS A -3 UNP P96382 EXPRESSION TAG SEQADV 4HCQ HIS A -2 UNP P96382 EXPRESSION TAG SEQADV 4HCQ HIS A -1 UNP P96382 EXPRESSION TAG SEQADV 4HCQ HIS A 0 UNP P96382 EXPRESSION TAG SEQRES 1 A 501 HIS HIS HIS HIS HIS HIS MET THR PHE PRO GLY ASP THR SEQRES 2 A 501 ALA VAL LEU VAL LEU ALA ALA GLY PRO GLY THR ARG MET SEQRES 3 A 501 ARG SER ASP THR PRO LYS VAL LEU HIS THR LEU ALA GLY SEQRES 4 A 501 ARG SER MET LEU SER HIS VAL LEU HIS ALA ILE ALA LYS SEQRES 5 A 501 LEU ALA PRO GLN ARG LEU ILE VAL VAL LEU GLY HIS ASP SEQRES 6 A 501 HIS GLN ARG ILE ALA PRO LEU VAL GLY GLU LEU ALA ASP SEQRES 7 A 501 THR LEU GLY ARG THR ILE ASP VAL ALA LEU GLN ASP ARG SEQRES 8 A 501 PRO LEU GLY THR GLY HIS ALA VAL LEU CYS GLY LEU SER SEQRES 9 A 501 ALA LEU PRO ASP ASP TYR ALA GLY ASN VAL VAL VAL THR SEQRES 10 A 501 SER GLY ASP THR PRO LEU LEU ASP ALA ASP THR LEU ALA SEQRES 11 A 501 ASP LEU ILE ALA THR HIS ARG ALA VAL SER ALA ALA VAL SEQRES 12 A 501 THR VAL LEU THR THR THR LEU ASP ASP PRO PHE GLY TYR SEQRES 13 A 501 GLY ARG ILE LEU ARG THR GLN ASP HIS GLU VAL MET ALA SEQRES 14 A 501 ILE VAL GLU GLN THR ASP ALA THR PRO SER GLN ARG GLU SEQRES 15 A 501 ILE ARG GLU VAL ASN ALA GLY VAL TYR ALA PHE ASP ILE SEQRES 16 A 501 ALA ALA LEU ARG SER ALA LEU SER ARG LEU SER SER ASN SEQRES 17 A 501 ASN ALA GLN GLN GLU LEU TYR LEU THR ASP VAL ILE ALA SEQRES 18 A 501 ILE LEU ARG SER ASP GLY GLN THR VAL HIS ALA SER HIS SEQRES 19 A 501 VAL ASP ASP SER ALA LEU VAL ALA GLY VAL ASN ASN ARG SEQRES 20 A 501 VAL GLN LEU ALA GLU LEU ALA SER GLU LEU ASN ARG ARG SEQRES 21 A 501 VAL VAL ALA ALA HIS GLN LEU ALA GLY VAL THR VAL VAL SEQRES 22 A 501 ASP PRO ALA THR THR TRP ILE ASP VAL ASP VAL THR ILE SEQRES 23 A 501 GLY ARG ASP THR VAL ILE HIS PRO GLY THR GLN LEU LEU SEQRES 24 A 501 GLY ARG THR GLN ILE GLY GLY ARG CYS VAL VAL GLY PRO SEQRES 25 A 501 ASP THR THR LEU THR ASP VAL ALA VAL GLY ASP GLY ALA SEQRES 26 A 501 SER VAL VAL ARG THR HIS GLY SER SER SER SER ILE GLY SEQRES 27 A 501 ASP GLY ALA ALA VAL GLY PRO PHE THR TYR LEU ARG PRO SEQRES 28 A 501 GLY THR ALA LEU GLY ALA ASP GLY LYS LEU GLY ALA PHE SEQRES 29 A 501 VAL GLU VAL LYS ASN SER THR ILE GLY THR GLY THR LYS SEQRES 30 A 501 VAL PRO HIS LEU THR TYR VAL GLY ASP ALA ASP ILE GLY SEQRES 31 A 501 GLU TYR SER ASN ILE GLY ALA SER SER VAL PHE VAL ASN SEQRES 32 A 501 TYR ASP GLY THR SER LYS ARG ARG THR THR VAL GLY SER SEQRES 33 A 501 HIS VAL ARG THR GLY SER ASP THR MET PHE VAL ALA PRO SEQRES 34 A 501 VAL THR ILE GLY ASP GLY ALA TYR THR GLY ALA GLY THR SEQRES 35 A 501 VAL VAL ARG GLU ASP VAL PRO PRO GLY ALA LEU ALA VAL SEQRES 36 A 501 SER ALA GLY PRO GLN ARG ASN ILE GLU ASN TRP VAL GLN SEQRES 37 A 501 ARG LYS ARG PRO GLY SER PRO ALA ALA GLN ALA SER LYS SEQRES 38 A 501 ARG ALA SER GLU MET ALA CYS GLN GLN PRO THR GLN PRO SEQRES 39 A 501 PRO ASP ALA ASP GLN THR PRO HET GN1 A 501 19 HET GN1 A 502 19 HET CO A 503 1 HET MG A 504 1 HET MG A 505 1 HETNAM GN1 2-ACETAMIDO-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM CO COBALT (II) ION HETNAM MG MAGNESIUM ION HETSYN GN1 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D- HETSYN 2 GN1 GLUCOPYRANOSE; N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE; N- HETSYN 3 GN1 ACETYL-1-O-PHOSPHONO-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO- HETSYN 4 GN1 2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOSE; 2-ACETAMIDO-2- HETSYN 5 GN1 DEOXY-1-O-PHOSPHONO-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-1- HETSYN 6 GN1 O-PHOSPHONO-GLUCOSE FORMUL 2 GN1 2(C8 H16 N O9 P) FORMUL 4 CO CO 2+ FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *87(H2 O) HELIX 1 1 GLY A 17 ARG A 21 5 5 HELIX 2 2 PRO A 25 LEU A 28 5 4 HELIX 3 3 MET A 36 ALA A 48 1 13 HELIX 4 4 ASP A 59 LEU A 74 1 16 HELIX 5 5 GLY A 88 SER A 98 1 11 HELIX 6 6 ASP A 119 VAL A 133 1 15 HELIX 7 7 GLU A 166 ALA A 170 5 5 HELIX 8 8 THR A 171 GLU A 176 1 6 HELIX 9 9 ILE A 189 SER A 197 1 9 HELIX 10 10 TYR A 209 THR A 211 5 3 HELIX 11 11 ASP A 212 ASP A 220 1 9 HELIX 12 12 ASP A 231 ALA A 236 5 6 HELIX 13 13 ASN A 240 ALA A 262 1 23 HELIX 14 14 ASP A 268 ALA A 270 5 3 HELIX 15 15 ASN A 459 LYS A 464 1 6 SHEET 1 A 7 ASP A 79 LEU A 82 0 SHEET 2 A 7 ARG A 51 LEU A 56 1 N VAL A 54 O ASP A 79 SHEET 3 A 7 THR A 7 ALA A 13 1 N VAL A 11 O ILE A 53 SHEET 4 A 7 ASN A 107 SER A 112 1 O THR A 111 N LEU A 12 SHEET 5 A 7 GLU A 179 ASP A 188 -1 O PHE A 187 N VAL A 108 SHEET 6 A 7 VAL A 137 THR A 143 -1 N THR A 142 O VAL A 180 SHEET 7 A 7 VAL A 224 HIS A 228 1 O HIS A 225 N VAL A 139 SHEET 1 B 2 THR A 30 LEU A 37 0 SHEET 2 B 2 ARG A 34 SER A 35 -1 O ARG A 34 N LEU A 37 SHEET 1 C 2 ARG A 152 ARG A 155 0 SHEET 2 C 2 VAL A 161 VAL A 165 -1 O MET A 162 N LEU A 154 SHEET 1 D13 THR A 271 VAL A 266 0 SHEET 2 D13 VAL A 285 ILE A 286 1 O ILE A 286 N THR A 271 SHEET 3 D13 VAL A 303 VAL A 304 1 O VAL A 304 N VAL A 285 SHEET 4 D13 SER A 320 VAL A 321 1 O VAL A 321 N VAL A 303 SHEET 5 D13 ALA A 336 VAL A 337 1 O VAL A 337 N SER A 320 SHEET 6 D13 LYS A 354 LYS A 362 1 O LEU A 355 N ALA A 336 SHEET 7 D13 THR A 347 LEU A 349 1 N TYR A 342 O VAL A 359 SHEET 8 D13 THR A 324 ILE A 331 1 N HIS A 325 O THR A 347 SHEET 9 D13 THR A 347 LEU A 355 1 O THR A 347 N SER A 330 SHEET 10 D13 SER A 364 ILE A 366 1 O ILE A 366 N ALA A 348 SHEET 11 D13 ALA A 381 ILE A 389 1 O ILE A 389 N THR A 365 SHEET 12 D13 THR A 406 VAL A 408 1 O VAL A 408 N ASP A 382 SHEET 13 D13 THR A 425 ILE A 426 1 O ILE A 426 N THR A 407 SHEET 1 E 7 LYS A 371 GLY A 379 0 SHEET 2 E 7 LYS A 354 LYS A 362 1 N GLU A 360 O VAL A 378 SHEET 3 E 7 THR A 347 LEU A 349 1 N TYR A 342 O VAL A 359 SHEET 4 E 7 THR A 324 ILE A 331 1 N HIS A 325 O THR A 347 SHEET 5 E 7 THR A 308 VAL A 321 1 N ALA A 314 O ILE A 331 SHEET 6 E 7 GLN A 297 ILE A 298 1 N GLN A 297 O VAL A 321 SHEET 7 E 7 THR A 279 ILE A 286 1 N THR A 279 O ILE A 298 SHEET 1 F 9 THR A 425 ILE A 426 0 SHEET 2 F 9 THR A 406 VAL A 408 1 N THR A 407 O ILE A 426 SHEET 3 F 9 ALA A 381 ILE A 389 1 N ASP A 382 O VAL A 408 SHEET 4 F 9 SER A 364 ILE A 366 1 N THR A 365 O ILE A 389 SHEET 5 F 9 THR A 347 LEU A 355 1 N ALA A 348 O ILE A 366 SHEET 6 F 9 THR A 324 ILE A 331 1 N SER A 330 O THR A 347 SHEET 7 F 9 THR A 308 VAL A 321 1 N ALA A 314 O ILE A 331 SHEET 8 F 9 THR A 296 LEU A 293 1 N LEU A 293 O LEU A 310 SHEET 9 F 9 THR A 272 ILE A 280 1 N TRP A 273 O LEU A 292 SHEET 1 G 2 ASN A 388 ILE A 389 0 SHEET 2 G 2 ARG A 413 THR A 414 1 O THR A 414 N ASN A 388 SHEET 1 H 3 VAL A 394 VAL A 396 0 SHEET 2 H 3 MET A 419 VAL A 421 1 O PHE A 420 N VAL A 394 SHEET 3 H 3 VAL A 437 VAL A 438 1 O VAL A 438 N MET A 419 SHEET 1 I 2 TYR A 431 THR A 432 0 SHEET 2 I 2 LEU A 447 ALA A 448 1 O ALA A 448 N TYR A 431 LINK OD2 ASP A 114 MG MG A 505 1555 1555 2.53 LINK OD1 ASN A 239 MG MG A 505 1555 1555 2.79 LINK OD1 ASP A 417 CO CO A 503 1555 1555 2.45 LINK OD2 ASP A 417 CO CO A 503 1555 1555 1.74 LINK OD1 ASP A 417 CO CO A 503 1555 2555 2.74 LINK OD2 ASP A 417 CO CO A 503 1555 3555 2.47 LINK OD1 ASP A 417 MG MG A 504 1555 1555 2.18 LINK OD1 ASP A 417 MG MG A 504 1555 3555 2.17 LINK MG MG A 504 O HOH A 687 1555 1555 2.17 LINK MG MG A 504 O HOH A 687 1555 2555 1.73 LINK MG MG A 505 O HOH A 602 1555 1555 2.02 LINK MG MG A 505 O HOH A 604 1555 1555 2.52 LINK MG MG A 505 O HOH A 605 1555 1555 2.33 CISPEP 1 GLY A 338 PRO A 339 0 -4.69 CISPEP 2 ALA A 422 PRO A 423 0 3.99 CRYST1 79.270 79.270 276.730 90.00 90.00 120.00 H 3 9 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 0.012615 0.007283 0.000000 0.00000 SCALE2 0.000000 0.014567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003614 0.00000