HEADER TRANSFERASE 22-JUN-08 3DJ4 TITLE CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX TITLE 2 WITH URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE. 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, MT1046; 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, TRIMER, CELL SHAPE, CELL WALL KEYWDS 3 BIOGENESIS/DEGRADATION, CYTOPLASM, MAGNESIUM, METAL-BINDING, KEYWDS 4 MULTIFUNCTIONAL ENZYME, NUCLEOTIDYLTRANSFERASE, PEPTIDOGLYCAN KEYWDS 5 SYNTHESIS, TRANSFERASE, ACYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.K.VERMA,B.PRAKASH REVDAT 2 20-MAR-24 3DJ4 1 REMARK LINK REVDAT 1 19-MAY-09 3DJ4 0 JRNL AUTH A.PARIKH,S.K.VERMA,S.KHAN,B.PRAKASH,V.K.NANDICOORI JRNL TITL PKNB-MEDIATED PHOSPHORYLATION OF A NOVEL SUBSTRATE, JRNL TITL 2 N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE, MODULATES JRNL TITL 3 ITS ACETYLTRANSFERASE ACTIVITY. JRNL REF J.MOL.BIOL. V. 386 451 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19121323 JRNL DOI 10.1016/J.JMB.2008.12.031 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25333 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1267 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) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3374 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.86000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -1.29000 REMARK 3 B12 (A**2) : 0.43000 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): 0.283 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.166 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.945 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3473 ; 0.027 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4758 ; 2.544 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 8.467 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;31.116 ;23.456 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 517 ;15.849 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;22.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 588 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2603 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1486 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2270 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 158 ; 0.192 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.007 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 81 ; 0.243 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.147 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2358 ; 1.286 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3680 ; 2.125 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1247 ; 3.574 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1076 ; 5.457 ; 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 : 1.20 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 3DJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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) : 1.54179 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 : 25334 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 8000, 150MM NACL, 2MM MNCL2, 5% REMARK 280 GLYCEROL, 1,3-BUTANEDIOL, AMPPNP, MGCL2, DTT, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 39.30000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.68987 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 92.66667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 39.30000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 22.68987 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 92.66667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 39.30000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 22.68987 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.66667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.37973 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 185.33333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.37973 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 185.33333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.37973 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 185.33333 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: 16750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -183.0 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 78.60000 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 39.30000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 68.06960 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 HOH A4048 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4093 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4121 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 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 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: 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 PRO A 65 C - N - CD ANGL. DEV. = -14.7 DEGREES REMARK 500 ALA A 473 N - CA - C ANGL. DEV. = -16.3 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 62 -61.20 -133.37 REMARK 500 ILE A 63 -41.24 -28.58 REMARK 500 VAL A 67 -51.01 70.26 REMARK 500 THR A 115 77.50 -114.53 REMARK 500 SER A 134 71.90 36.65 REMARK 500 THR A 156 -171.29 -62.29 REMARK 500 ALA A 170 -152.47 -1.95 REMARK 500 PRO A 172 -92.97 -51.65 REMARK 500 GLN A 174 78.87 -64.87 REMARK 500 GLU A 176 -13.58 -48.94 REMARK 500 ASP A 277 -38.74 126.79 REMARK 500 ASP A 307 38.76 72.54 REMARK 500 ARG A 323 63.79 35.42 REMARK 500 SER A 328 63.58 38.72 REMARK 500 PHE A 340 55.91 72.36 REMARK 500 ASN A 363 53.19 38.06 REMARK 500 SER A 450 -29.23 -150.38 REMARK 500 PRO A 466 47.89 -70.59 REMARK 500 SER A 468 -128.22 87.28 REMARK 500 PRO A 469 -18.79 -43.42 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 HIS A 58 ASP A 59 -143.04 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 496 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 114 OD2 REMARK 620 2 ASN A 239 OD1 89.7 REMARK 620 3 UD1 A4000 O2A 85.5 89.5 REMARK 620 4 UD1 A4000 O1B 148.2 101.2 65.1 REMARK 620 5 HOH A4120 O 92.2 85.6 174.6 118.1 REMARK 620 6 HOH A4133 O 87.0 167.2 102.5 88.0 82.3 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 A 496 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UD1 A 4000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DIU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GLMU FROM MYCOBACTERIUM TUBERCULOSIS IN REMARK 900 COMPLEX WITH UMPPNP AND N-ACETYLGLUCOSAMINE-1-PHOSPHATE. DBREF 3DJ4 A 1 495 UNP P96382 GLMU_MYCTU 1 495 SEQRES 1 A 495 MET THR PHE PRO GLY ASP THR ALA VAL LEU VAL LEU ALA SEQRES 2 A 495 ALA GLY PRO GLY THR ARG MET ARG SER ASP THR PRO LYS SEQRES 3 A 495 VAL LEU HIS THR LEU ALA GLY ARG SER MET LEU SER HIS SEQRES 4 A 495 VAL LEU HIS ALA ILE ALA LYS LEU ALA PRO GLN ARG LEU SEQRES 5 A 495 ILE VAL VAL LEU GLY HIS ASP HIS GLN ARG ILE ALA PRO SEQRES 6 A 495 LEU VAL GLY GLU LEU ALA ASP THR LEU GLY ARG THR ILE SEQRES 7 A 495 ASP VAL ALA LEU GLN ASP ARG PRO LEU GLY THR GLY HIS SEQRES 8 A 495 ALA VAL LEU CYS GLY LEU SER ALA LEU PRO ASP ASP TYR SEQRES 9 A 495 ALA GLY ASN VAL VAL VAL THR SER GLY ASP THR PRO LEU SEQRES 10 A 495 LEU ASP ALA ASP THR LEU ALA ASP LEU ILE ALA THR HIS SEQRES 11 A 495 ARG ALA VAL SER ALA ALA VAL THR VAL LEU THR THR THR SEQRES 12 A 495 LEU ASP ASP PRO PHE GLY TYR GLY ARG ILE LEU ARG THR SEQRES 13 A 495 GLN ASP HIS GLU VAL MET ALA ILE VAL GLU GLN THR ASP SEQRES 14 A 495 ALA THR PRO SER GLN ARG GLU ILE ARG GLU VAL ASN ALA SEQRES 15 A 495 GLY VAL TYR ALA PHE ASP ILE ALA ALA LEU ARG SER ALA SEQRES 16 A 495 LEU SER ARG LEU SER SER ASN ASN ALA GLN GLN GLU LEU SEQRES 17 A 495 TYR LEU THR ASP VAL ILE ALA ILE LEU ARG SER ASP GLY SEQRES 18 A 495 GLN THR VAL HIS ALA SER HIS VAL ASP ASP SER ALA LEU SEQRES 19 A 495 VAL ALA GLY VAL ASN ASN ARG VAL GLN LEU ALA GLU LEU SEQRES 20 A 495 ALA SER GLU LEU ASN ARG ARG VAL VAL ALA ALA HIS GLN SEQRES 21 A 495 LEU ALA GLY VAL THR VAL VAL ASP PRO ALA THR THR TRP SEQRES 22 A 495 ILE ASP VAL ASP VAL THR ILE GLY ARG ASP THR VAL ILE SEQRES 23 A 495 HIS PRO GLY THR GLN LEU LEU GLY ARG THR GLN ILE GLY SEQRES 24 A 495 GLY ARG CYS VAL VAL GLY PRO ASP THR THR LEU THR ASP SEQRES 25 A 495 VAL ALA VAL GLY ASP GLY ALA SER VAL VAL ARG THR HIS SEQRES 26 A 495 GLY SER SER SER SER ILE GLY ASP GLY ALA ALA VAL GLY SEQRES 27 A 495 PRO PHE THR TYR LEU ARG PRO GLY THR ALA LEU GLY ALA SEQRES 28 A 495 ASP GLY LYS LEU GLY ALA PHE VAL GLU VAL LYS ASN SER SEQRES 29 A 495 THR ILE GLY THR GLY THR LYS VAL PRO HIS LEU THR TYR SEQRES 30 A 495 VAL GLY ASP ALA ASP ILE GLY GLU TYR SER ASN ILE GLY SEQRES 31 A 495 ALA SER SER VAL PHE VAL ASN TYR ASP GLY THR SER LYS SEQRES 32 A 495 ARG ARG THR THR VAL GLY SER HIS VAL ARG THR GLY SER SEQRES 33 A 495 ASP THR MET PHE VAL ALA PRO VAL THR ILE GLY ASP GLY SEQRES 34 A 495 ALA TYR THR GLY ALA GLY THR VAL VAL ARG GLU ASP VAL SEQRES 35 A 495 PRO PRO GLY ALA LEU ALA VAL SER ALA GLY PRO GLN ARG SEQRES 36 A 495 ASN ILE GLU ASN TRP VAL GLN ARG LYS ARG PRO GLY SER SEQRES 37 A 495 PRO ALA ALA GLN ALA SER LYS ARG ALA SER GLU MET ALA SEQRES 38 A 495 CYS GLN GLN PRO THR GLN PRO PRO ASP ALA ASP GLN THR SEQRES 39 A 495 PRO HET MG A 496 1 HET CO A 497 1 HET UD1 A4000 39 HETNAM MG MAGNESIUM ION HETNAM CO COBALT (II) ION HETNAM UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE FORMUL 2 MG MG 2+ FORMUL 3 CO CO 2+ FORMUL 4 UD1 C17 H27 N3 O17 P2 FORMUL 5 HOH *147(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 ALA A 64 1 6 HELIX 5 5 GLU A 69 LEU A 74 1 6 HELIX 6 6 GLY A 88 SER A 98 1 11 HELIX 7 7 ASP A 119 VAL A 133 1 15 HELIX 8 8 ILE A 189 SER A 197 1 9 HELIX 9 9 TYR A 209 THR A 211 5 3 HELIX 10 10 ASP A 212 ASP A 220 1 9 HELIX 11 11 ASP A 231 ALA A 236 5 6 HELIX 12 12 ASN A 240 ALA A 262 1 23 HELIX 13 13 ASP A 268 ALA A 270 5 3 HELIX 14 14 ASN A 459 ARG A 465 1 7 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 9 O ILE A 53 SHEET 4 A 7 ASN A 107 SER A 112 1 O VAL A 109 N LEU A 10 SHEET 5 A 7 GLU A 179 ASP A 188 -1 O TYR A 185 N VAL A 110 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 SER A 227 N VAL A 139 SHEET 1 B 2 THR A 30 LEU A 31 0 SHEET 2 B 2 ARG A 34 SER A 35 -1 O ARG A 34 N LEU A 31 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 D 7 THR A 265 VAL A 266 0 SHEET 2 D 7 VAL A 285 ILE A 286 1 O ILE A 286 N THR A 265 SHEET 3 D 7 VAL A 303 VAL A 304 1 O VAL A 304 N VAL A 285 SHEET 4 D 7 SER A 320 VAL A 321 1 O VAL A 321 N VAL A 303 SHEET 5 D 7 ALA A 336 VAL A 337 1 O VAL A 337 N SER A 320 SHEET 6 D 7 LYS A 354 ALA A 357 1 O LEU A 355 N ALA A 336 SHEET 7 D 7 LYS A 371 HIS A 374 1 O VAL A 372 N GLY A 356 SHEET 1 E 7 THR A 272 ILE A 274 0 SHEET 2 E 7 THR A 290 LEU A 293 1 O LEU A 292 N TRP A 273 SHEET 3 E 7 THR A 309 VAL A 315 1 O LEU A 310 N LEU A 293 SHEET 4 E 7 THR A 324 ILE A 331 1 O GLY A 326 N THR A 309 SHEET 5 E 7 THR A 341 LEU A 343 1 O THR A 341 N HIS A 325 SHEET 6 E 7 VAL A 359 LYS A 362 1 O VAL A 361 N TYR A 342 SHEET 7 E 7 TYR A 377 GLY A 379 1 O VAL A 378 N GLU A 360 SHEET 1 F 9 THR A 279 ILE A 280 0 SHEET 2 F 9 GLN A 297 ILE A 298 1 O ILE A 298 N THR A 279 SHEET 3 F 9 THR A 309 VAL A 315 1 O VAL A 315 N GLN A 297 SHEET 4 F 9 THR A 324 ILE A 331 1 O GLY A 326 N THR A 309 SHEET 5 F 9 ALA A 348 LEU A 349 1 O LEU A 349 N SER A 330 SHEET 6 F 9 THR A 365 ILE A 366 1 O ILE A 366 N ALA A 348 SHEET 7 F 9 ALA A 381 ILE A 383 1 O ILE A 383 N THR A 365 SHEET 8 F 9 THR A 406 VAL A 408 1 O THR A 406 N ASP A 382 SHEET 9 F 9 THR A 425 ILE A 426 1 O ILE A 426 N THR A 407 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 496 1555 1555 2.03 LINK OD1 ASN A 239 MG MG A 496 1555 1555 1.98 LINK MG MG A 496 O2A UD1 A4000 1555 1555 2.09 LINK MG MG A 496 O1B UD1 A4000 1555 1555 1.98 LINK MG MG A 496 O HOH A4120 1555 1555 2.34 LINK MG MG A 496 O HOH A4133 1555 1555 2.07 CISPEP 1 GLY A 338 PRO A 339 0 -1.41 CISPEP 2 ALA A 422 PRO A 423 0 -10.72 CISPEP 3 ALA A 471 GLN A 472 0 10.81 SITE 1 AC1 4 ASP A 114 ASN A 239 HOH A4120 HOH A4133 SITE 1 AC2 1 PHE A 340 SITE 1 AC3 27 LEU A 12 ALA A 13 ALA A 14 GLY A 15 SITE 2 AC3 27 LYS A 26 GLN A 83 PRO A 86 LEU A 87 SITE 3 AC3 27 GLY A 88 THR A 89 ALA A 92 SER A 112 SITE 4 AC3 27 GLY A 113 ASP A 114 TYR A 150 GLY A 151 SITE 5 AC3 27 GLU A 166 ASN A 181 ALA A 182 THR A 211 SITE 6 AC3 27 ASN A 239 HOH A4001 HOH A4019 HOH A4066 SITE 7 AC3 27 HOH A4076 HOH A4120 HOH A4133 CRYST1 78.600 78.600 278.000 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 0.012723 0.007345 0.000000 0.00000 SCALE2 0.000000 0.014691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003597 0.00000