HEADER TRANSFERASE 28-SEP-07 2VD4 TITLE STRUCTURE OF SMALL-MOLECULE INHIBITOR OF GLMU FROM HAEMOPHILUS TITLE 2 INFLUENZAE REVEALS AN ALLOSTERIC BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PROTEIN GLMU; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLMU FROM HAEMOPHILIS INFLUENZAE; COMPND 5 EC: 2.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLMU, INHIBITOR, MAGNESIUM, CELL SHAPE, PEPTIDOGLYCAN SYNTHESIS, KEYWDS 2 ALLOSTERIC, TRANSFERASE, ACTIVE SITE, METAL-BINDING, CELL WALL KEYWDS 3 BIOGENESIS/DEGRADATION, MULTIFUNCTIONAL ENZYME, KEYWDS 4 NUCLEOTIDYLTRANSFERASE, ACYLTRANSFERASE, URIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR I.MOCHALKIN,S.LIGHTLE,L.MCDOWELL REVDAT 5 13-DEC-23 2VD4 1 REMARK LINK REVDAT 4 13-JUL-11 2VD4 1 VERSN REVDAT 3 24-FEB-09 2VD4 1 VERSN REVDAT 2 04-MAR-08 2VD4 1 JRNL REVDAT 1 15-JAN-08 2VD4 0 JRNL AUTH I.MOCHALKIN,S.LIGHTLE,L.NARASIMHAN,D.BORNEMEIER,M.MELNICK, JRNL AUTH 2 S.VANDERROEST,L.MCDOWELL JRNL TITL STRUCTURE OF A SMALL-MOLECULE INHIBITOR COMPLEXED WITH GLMU JRNL TITL 2 FROM HAEMOPHILUS INFLUENZAE REVEALS AN ALLOSTERIC BINDING JRNL TITL 3 SITE. JRNL REF PROTEIN SCI. V. 17 577 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18218712 JRNL DOI 10.1110/PS.073271408 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 111.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 52488 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3549 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3414 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.56000 REMARK 3 B22 (A**2) : 0.56000 REMARK 3 B33 (A**2) : -0.85000 REMARK 3 B12 (A**2) : 0.28000 REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.144 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3558 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3289 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4811 ; 1.270 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7667 ; 0.931 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 5.838 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 555 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3925 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 636 ; 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): 2217 ; 1.061 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3573 ; 1.760 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1341 ; 1.405 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1238 ; 2.322 ; 3.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 456 REMARK 3 ORIGIN FOR THE GROUP (A): 69.8302 41.7731 19.1352 REMARK 3 T TENSOR REMARK 3 T11: 0.0092 T22: 0.0016 REMARK 3 T33: 0.0107 T12: -0.0038 REMARK 3 T13: -0.0036 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.1354 L22: 0.0087 REMARK 3 L33: 0.2353 L12: 0.0112 REMARK 3 L13: 0.1390 L23: 0.0068 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: -0.0178 S13: 0.0076 REMARK 3 S21: 0.0024 S22: -0.0052 S23: -0.0062 REMARK 3 S31: -0.0227 S32: -0.0049 S33: 0.0051 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 RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1290034004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX, REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2V0H REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7-1.8 M AMMONIUM SULFATE, 2% PEG REMARK 280 -400, AND 0.1M MES PH 5.4-6.1, PH 5.9 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 54.09300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.23061 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 109.14333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 54.09300 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 31.23061 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 109.14333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 54.09300 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 31.23061 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 109.14333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 54.09300 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 31.23061 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 109.14333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 54.09300 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 31.23061 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 109.14333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 54.09300 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 31.23061 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 109.14333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.46122 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 218.28667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 62.46122 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 218.28667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 62.46122 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 218.28667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 62.46122 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 218.28667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 62.46122 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 218.28667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 62.46122 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 218.28667 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 65320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.4 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 108.18600 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 54.09300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 93.69182 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 MG MG A1463 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A1464 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 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 454 REMARK 465 LYS A 455 REMARK 465 LYS A 456 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 ARG A 63 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 VAL A 301 CG1 - CB - CG2 ANGL. DEV. = 10.0 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 ALA A 12 26.65 -144.93 REMARK 500 ASN A 124 13.03 59.30 REMARK 500 ASN A 146 -131.27 65.94 REMARK 500 ASP A 388 92.81 -69.30 REMARK 500 ALA A 390 -114.11 -96.97 REMARK 500 PRO A 452 74.48 -59.48 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 A1463 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 406 OD2 REMARK 620 2 ASP A 406 OD2 95.1 REMARK 620 3 ASP A 406 OD2 95.6 95.6 REMARK 620 4 HOH A2244 O 87.8 88.3 174.6 REMARK 620 5 HOH A2244 O 173.9 88.2 89.1 87.2 REMARK 620 6 HOH A2244 O 88.7 174.0 88.7 87.2 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1464 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 406 OD1 REMARK 620 2 ASP A 406 OD1 91.7 REMARK 620 3 ASP A 406 OD1 91.6 91.7 REMARK 620 4 HOH A2228 O 174.9 92.4 85.2 REMARK 620 5 HOH A2228 O 85.0 174.9 92.2 91.1 REMARK 620 6 HOH A2228 O 92.2 85.2 175.2 91.2 91.1 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P21 A 1454 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1455 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1456 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1457 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1458 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1459 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1464 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V0I RELATED DB: PDB REMARK 900 CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE REMARK 900 POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE REMARK 900 URIDYLTRANSFERASE (GLMU) REMARK 900 RELATED ID: 2V0L RELATED DB: PDB REMARK 900 CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE REMARK 900 POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE REMARK 900 URIDYLTRANSFERASE (GLMU) REMARK 900 RELATED ID: 2V0H RELATED DB: PDB REMARK 900 CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE REMARK 900 POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE REMARK 900 URIDYLTRANSFERASE (GLMU) REMARK 900 RELATED ID: 2V0J RELATED DB: PDB REMARK 900 CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE REMARK 900 POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE REMARK 900 URIDYLTRANSFERASE (GLMU) REMARK 900 RELATED ID: 2V0K RELATED DB: PDB REMARK 900 CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE REMARK 900 POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE REMARK 900 URIDYLTRANSFERASE (GLMU) DBREF 2VD4 A 1 456 UNP P43889 GLMU_HAEIN 1 456 SEQRES 1 A 456 MET THR LYS LYS ALA LEU SER ALA VAL ILE LEU ALA ALA SEQRES 2 A 456 GLY LYS GLY THR ARG MET TYR SER ASP LEU PRO LYS VAL SEQRES 3 A 456 LEU HIS THR ILE ALA GLY LYS PRO MET VAL LYS HIS VAL SEQRES 4 A 456 ILE ASP THR ALA HIS GLN LEU GLY SER GLU ASN ILE HIS SEQRES 5 A 456 LEU ILE TYR GLY HIS GLY GLY ASP LEU MET ARG THR HIS SEQRES 6 A 456 LEU ALA ASN GLU GLN VAL ASN TRP VAL LEU GLN THR GLU SEQRES 7 A 456 GLN LEU GLY THR ALA HIS ALA VAL GLN GLN ALA ALA PRO SEQRES 8 A 456 PHE PHE LYS ASP ASN GLU ASN ILE VAL VAL LEU TYR GLY SEQRES 9 A 456 ASP ALA PRO LEU ILE THR LYS GLU THR LEU GLU LYS LEU SEQRES 10 A 456 ILE GLU ALA LYS PRO GLU ASN GLY ILE ALA LEU LEU THR SEQRES 11 A 456 VAL ASN LEU ASP ASN PRO THR GLY TYR GLY ARG ILE ILE SEQRES 12 A 456 ARG GLU ASN GLY ASN VAL VAL ALA ILE VAL GLU GLN LYS SEQRES 13 A 456 ASP ALA ASN ALA GLU GLN LEU ASN ILE LYS GLU VAL ASN SEQRES 14 A 456 THR GLY VAL MET VAL SER ASP GLY ALA SER PHE LYS LYS SEQRES 15 A 456 TRP LEU ALA ARG VAL GLY ASN ASN ASN ALA GLN GLY GLU SEQRES 16 A 456 TYR TYR LEU THR ASP LEU ILE ALA LEU ALA ASN GLN ASP SEQRES 17 A 456 ASN CYS GLN VAL VAL ALA VAL GLN ALA THR ASP VAL MET SEQRES 18 A 456 GLU VAL GLU GLY ALA ASN ASN ARG LEU GLN LEU ALA ALA SEQRES 19 A 456 LEU GLU ARG TYR PHE GLN ASN LYS GLN ALA SER LYS LEU SEQRES 20 A 456 LEU LEU GLU GLY VAL MET ILE TYR ASP PRO ALA ARG PHE SEQRES 21 A 456 ASP LEU ARG GLY THR LEU GLU HIS GLY LYS ASP VAL GLU SEQRES 22 A 456 ILE ASP VAL ASN VAL ILE ILE GLU GLY ASN VAL LYS LEU SEQRES 23 A 456 GLY ASP ARG VAL LYS ILE GLY THR GLY CYS VAL LEU LYS SEQRES 24 A 456 ASN VAL VAL ILE GLY ASN ASP VAL GLU ILE LYS PRO TYR SEQRES 25 A 456 SER VAL LEU GLU ASP SER ILE VAL GLY GLU LYS ALA ALA SEQRES 26 A 456 ILE GLY PRO PHE SER ARG LEU ARG PRO GLY ALA GLU LEU SEQRES 27 A 456 ALA ALA GLU THR HIS VAL GLY ASN PHE VAL GLU ILE LYS SEQRES 28 A 456 LYS SER THR VAL GLY LYS GLY SER LYS VAL ASN HIS LEU SEQRES 29 A 456 THR TYR VAL GLY ASP SER GLU ILE GLY SER ASN CYS ASN SEQRES 30 A 456 ILE GLY ALA GLY VAL ILE THR CYS ASN TYR ASP GLY ALA SEQRES 31 A 456 ASN LYS PHE LYS THR ILE ILE GLY ASP ASP VAL PHE VAL SEQRES 32 A 456 GLY SER ASP THR GLN LEU VAL ALA PRO VAL LYS VAL ALA SEQRES 33 A 456 ASN GLY ALA THR ILE GLY ALA GLY THR THR ILE THR ARG SEQRES 34 A 456 ASP VAL GLY GLU ASN GLU LEU VAL ILE THR ARG VAL ALA SEQRES 35 A 456 GLN ARG HIS ILE GLN GLY TRP GLN ARG PRO ILE LYS LYS SEQRES 36 A 456 LYS HET P21 A1454 29 HET SO4 A1455 5 HET SO4 A1456 5 HET SO4 A1457 5 HET SO4 A1458 5 HET SO4 A1459 5 HET PG4 A1460 13 HET PG4 A1461 13 HET PGE A1462 10 HET MG A1463 1 HET MG A1464 1 HET SO4 A1465 5 HETNAM P21 4-CHLORO-N-(3-METHOXYPROPYL)-N-[(3S)-1-(2-PHENYLETHYL) HETNAM 2 P21 PIPERIDIN-3-YL]BENZAMIDE HETNAM SO4 SULFATE ION HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM MG MAGNESIUM ION FORMUL 2 P21 C24 H31 CL N2 O2 FORMUL 3 SO4 6(O4 S 2-) FORMUL 8 PG4 2(C8 H18 O5) FORMUL 10 PGE C6 H14 O4 FORMUL 11 MG 2(MG 2+) FORMUL 14 HOH *291(H2 O) HELIX 1 1 GLY A 16 TYR A 20 5 5 HELIX 2 2 PRO A 24 LEU A 27 5 4 HELIX 3 3 MET A 35 LEU A 46 1 12 HELIX 4 4 GLY A 58 LEU A 66 1 9 HELIX 5 5 GLY A 81 ALA A 90 1 10 HELIX 6 6 PRO A 91 PHE A 93 5 3 HELIX 7 7 THR A 110 LYS A 121 1 12 HELIX 8 8 GLU A 154 ALA A 158 5 5 HELIX 9 9 ASN A 159 ASN A 164 1 6 HELIX 10 10 GLY A 177 ALA A 185 1 9 HELIX 11 11 TYR A 197 THR A 199 5 3 HELIX 12 12 ASP A 200 ASP A 208 1 9 HELIX 13 13 VAL A 220 GLU A 224 5 5 HELIX 14 14 ASN A 228 GLY A 251 1 24 HELIX 15 15 ASP A 256 ALA A 258 5 3 SHEET 1 AA 7 ASN A 72 LEU A 75 0 SHEET 2 AA 7 ILE A 51 TYR A 55 1 O ILE A 51 N ASN A 72 SHEET 3 AA 7 LEU A 6 LEU A 11 1 O ALA A 8 N HIS A 52 SHEET 4 AA 7 ASN A 98 TYR A 103 1 O ASN A 98 N SER A 7 SHEET 5 AA 7 GLU A 167 ASP A 176 -1 O MET A 173 N VAL A 101 SHEET 6 AA 7 ILE A 126 ASN A 132 -1 O ALA A 127 N VAL A 174 SHEET 7 AA 7 VAL A 212 GLN A 216 1 O VAL A 213 N LEU A 128 SHEET 1 AB 2 THR A 29 ILE A 30 0 SHEET 2 AB 2 LYS A 33 PRO A 34 -1 O LYS A 33 N ILE A 30 SHEET 1 AC 2 ARG A 141 GLU A 145 0 SHEET 2 AC 2 ASN A 148 VAL A 153 -1 O ASN A 148 N GLU A 145 SHEET 1 AD 8 MET A 253 ILE A 254 0 SHEET 2 AD 8 GLU A 273 ILE A 274 1 N ILE A 274 O MET A 253 SHEET 3 AD 8 LYS A 291 ILE A 292 1 N ILE A 292 O GLU A 273 SHEET 4 AD 8 GLU A 308 ILE A 309 1 N ILE A 309 O LYS A 291 SHEET 5 AD 8 ALA A 325 ILE A 326 1 N ILE A 326 O GLU A 308 SHEET 6 AD 8 HIS A 343 LYS A 351 1 N VAL A 344 O ALA A 325 SHEET 7 AD 8 SER A 330 LEU A 332 1 O ARG A 331 N ILE A 350 SHEET 8 AD 8 VAL A 314 VAL A 320 1 O VAL A 314 N LEU A 332 SHEET 1 AE11 MET A 253 ILE A 254 0 SHEET 2 AE11 GLU A 273 ILE A 274 1 N ILE A 274 O MET A 253 SHEET 3 AE11 LYS A 291 ILE A 292 1 N ILE A 292 O GLU A 273 SHEET 4 AE11 GLU A 308 ILE A 309 1 N ILE A 309 O LYS A 291 SHEET 5 AE11 ALA A 325 ILE A 326 1 N ILE A 326 O GLU A 308 SHEET 6 AE11 HIS A 343 LYS A 351 1 N VAL A 344 O ALA A 325 SHEET 7 AE11 LYS A 360 GLY A 368 1 O VAL A 361 N GLY A 345 SHEET 8 AE11 ASN A 377 ILE A 378 1 O ILE A 378 N ASN A 362 SHEET 9 AE11 PHE A 402 VAL A 403 1 N VAL A 403 O ASN A 377 SHEET 10 AE11 THR A 420 ILE A 421 1 N ILE A 421 O PHE A 402 SHEET 11 AE11 LEU A 436 VAL A 437 1 N VAL A 437 O THR A 420 SHEET 1 AF 3 ILE A 383 ASN A 386 0 SHEET 2 AF 3 GLN A 408 ALA A 411 1 O LEU A 409 N CYS A 385 SHEET 3 AF 3 THR A 426 ILE A 427 1 O ILE A 427 N VAL A 410 LINK OD2 ASP A 406 MG MG A1463 1555 1555 2.09 LINK OD2 ASP A 406 MG MG A1463 2655 1555 2.09 LINK OD2 ASP A 406 MG MG A1463 3665 1555 2.08 LINK OD1 ASP A 406 MG MG A1464 3665 1555 2.17 LINK OD1 ASP A 406 MG MG A1464 1555 1555 2.17 LINK OD1 ASP A 406 MG MG A1464 2655 1555 2.17 LINK MG MG A1463 O HOH A2244 1555 2655 2.17 LINK MG MG A1463 O HOH A2244 1555 3665 2.16 LINK MG MG A1463 O HOH A2244 1555 1555 2.16 LINK MG MG A1464 O HOH A2228 1555 2655 2.11 LINK MG MG A1464 O HOH A2228 1555 3665 2.11 LINK MG MG A1464 O HOH A2228 1555 1555 2.11 CISPEP 1 GLY A 327 PRO A 328 0 -1.97 CISPEP 2 ALA A 411 PRO A 412 0 -2.68 SITE 1 AC1 9 TYR A 139 ASN A 169 VAL A 223 GLU A 224 SITE 2 AC1 9 GLY A 225 GLN A 231 LEU A 235 SO4 A1458 SITE 3 AC1 9 HOH A2280 SITE 1 AC2 6 LYS A 360 ASN A 362 HIS A 363 HOH A2225 SITE 2 AC2 6 HOH A2281 HOH A2282 SITE 1 AC3 3 LYS A 15 HIS A 57 GLY A 58 SITE 1 AC4 4 ASN A 377 ARG A 451 HOH A2221 HOH A2284 SITE 1 AC5 3 ASN A 227 GLN A 231 P21 A1454 SITE 1 AC6 4 HIS A 57 GLU A 78 GLN A 79 HOH A2285 SITE 1 AC7 5 ARG A 331 ARG A 333 PRO A 334 HOH A2290 SITE 2 AC7 5 HOH A2291 SITE 1 AC8 10 GLU A 49 ASN A 50 GLN A 70 VAL A 71 SITE 2 AC8 10 ASN A 72 PHE A 92 TYR A 387 HOH A2023 SITE 3 AC8 10 HOH A2024 HOH A2286 SITE 1 AC9 8 ASN A 72 ASN A 386 ASP A 388 PHE A 402 SITE 2 AC9 8 ALA A 423 HOH A2252 HOH A2287 HOH A2288 SITE 1 BC1 9 VAL A 153 ASP A 157 ASN A 159 GLN A 162 SITE 2 BC1 9 ASN A 189 ASN A 191 ALA A 192 GLY A 194 SITE 3 BC1 9 HOH A2289 SITE 1 BC2 2 ASP A 406 HOH A2244 SITE 1 BC3 2 ASP A 406 HOH A2228 CRYST1 108.186 108.186 327.430 90.00 90.00 120.00 H 3 2 18 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 0.009243 0.005337 0.000000 0.00000 SCALE2 0.000000 0.010673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003054 0.00000