HEADER HYDROLASE 29-JUL-10 3O6Z TITLE STRUCTURE OF THE D152A E.COLI GDP-MANNOSE HYDROLASE (YFFH) IN COMPLEX TITLE 2 WITH MG++ COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDP-MANNOSE PYROPHOSPHATASE NUDK; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2467, JW2451, NUDK, YFFH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS NUDIX, GDP_MANNOSE, HYDROLASE, BIOFILM EXPDTA X-RAY DIFFRACTION AUTHOR L.M.AMZEL,S.B.GABELLI,A.N.BOTO REVDAT 4 06-SEP-23 3O6Z 1 REMARK SEQADV LINK REVDAT 3 10-AUG-11 3O6Z 1 JRNL REVDAT 2 13-JUL-11 3O6Z 1 JRNL REVDAT 1 11-MAY-11 3O6Z 0 JRNL AUTH A.N.BOTO,W.XU,J.JAKONCIC,A.PANNURI,T.ROMEO,M.J.BESSMAN, JRNL AUTH 2 S.B.GABELLI,L.M.AMZEL JRNL TITL STRUCTURAL STUDIES OF THE NUDIX GDP-MANNOSE HYDROLASE FROM JRNL TITL 2 E. COLI REVEALS A NEW MOTIF FOR MANNOSE RECOGNITION. JRNL REF PROTEINS V. 79 2455 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21638333 JRNL DOI 10.1002/PROT.23069 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 25302 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1280 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) : 1819 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2969 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.92000 REMARK 3 B22 (A**2) : -0.91000 REMARK 3 B33 (A**2) : -1.01000 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): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.966 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3043 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4092 ; 1.438 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 6.561 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;36.408 ;24.771 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 566 ;15.657 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.610 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2245 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1439 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2014 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 305 ; 0.174 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.049 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 34 ; 0.273 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.226 ; 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): 1892 ; 0.777 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2951 ; 1.226 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1293 ; 1.819 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1141 ; 2.634 ; 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 : 3 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 2 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 11.0730 36.9910 40.6010 REMARK 3 T TENSOR REMARK 3 T11: -0.0694 T22: -0.1076 REMARK 3 T33: -0.0983 T12: 0.0045 REMARK 3 T13: -0.0483 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 2.6885 L22: 1.1555 REMARK 3 L33: 1.7739 L12: 0.1957 REMARK 3 L13: 0.0945 L23: -0.3113 REMARK 3 S TENSOR REMARK 3 S11: -0.0746 S12: -0.1037 S13: 0.2837 REMARK 3 S21: 0.0169 S22: -0.0637 S23: 0.0118 REMARK 3 S31: -0.2570 S32: 0.1329 S33: 0.1384 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 150 A 191 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1790 38.6050 29.0870 REMARK 3 T TENSOR REMARK 3 T11: -0.0510 T22: 0.1021 REMARK 3 T33: -0.0476 T12: -0.0372 REMARK 3 T13: 0.0144 T23: 0.1109 REMARK 3 L TENSOR REMARK 3 L11: 4.2794 L22: 5.3057 REMARK 3 L33: 1.2306 L12: 1.1314 REMARK 3 L13: -1.5794 L23: 0.5040 REMARK 3 S TENSOR REMARK 3 S11: -0.0216 S12: 0.6127 S13: 0.1758 REMARK 3 S21: -0.4536 S22: -0.1253 S23: -0.5711 REMARK 3 S31: -0.0801 S32: 0.4116 S33: 0.1469 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 191 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8240 25.6790 32.1080 REMARK 3 T TENSOR REMARK 3 T11: -0.1146 T22: -0.1597 REMARK 3 T33: -0.1243 T12: 0.0062 REMARK 3 T13: -0.0027 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 1.3494 L22: 0.6587 REMARK 3 L33: 2.0340 L12: 0.3599 REMARK 3 L13: 0.7106 L23: -0.1286 REMARK 3 S TENSOR REMARK 3 S11: -0.0696 S12: 0.0853 S13: -0.0319 REMARK 3 S21: -0.0870 S22: 0.0383 S23: -0.0433 REMARK 3 S31: 0.0727 S32: 0.1437 S33: 0.0313 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 REMARK 4 REMARK 4 3O6Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 FR-E+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26521 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 20.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 3O52 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-26% PEG 3350, 0.2 M MGCL2, 0.1 M REMARK 280 TRIS PH 8.5, 4 MM GDP-MANNOSE AT A RATIO OF 1:1 PROTEIN: REMARK 280 RESERVOIR, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.45800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.80600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.66650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.80600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.45800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.66650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 106 REMARK 465 ALA A 142 REMARK 465 ASN A 143 REMARK 465 ALA A 144 REMARK 465 GLY A 145 REMARK 465 GLY A 146 REMARK 465 GLY A 147 REMARK 465 VAL A 148 REMARK 465 GLU A 149 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLU B 33 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 44 CA 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 LEU A 189 C LEU A 189 O 0.117 REMARK 500 ARG B 44 CA ARG B 44 CB 0.646 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 ASP A 191 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 44 CB - CA - C ANGL. DEV. = 30.6 DEGREES REMARK 500 LEU B 158 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 LEU B 179 CA - CB - CG ANGL. DEV. = 17.3 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 GLN A 3 -85.84 19.30 REMARK 500 TYR A 17 -64.86 -162.09 REMARK 500 LEU A 88 86.76 -67.48 REMARK 500 GLU A 151 -168.33 -118.08 REMARK 500 ARG A 173 38.38 -145.95 REMARK 500 HIS A 188 -4.51 89.25 REMARK 500 ASP B 15 74.16 -150.93 REMARK 500 TYR B 17 -51.92 -128.37 REMARK 500 GLU B 149 -125.62 54.39 REMARK 500 ARG B 173 35.18 -145.01 REMARK 500 HIS B 188 -1.38 67.14 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 85 O REMARK 620 2 GLU A 104 OE2 76.2 REMARK 620 3 HOH A 311 O 99.0 104.8 REMARK 620 4 HOH A 324 O 167.1 105.7 92.9 REMARK 620 5 HOH A 417 O 83.5 83.0 172.2 84.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 85 O REMARK 620 2 GLU B 104 OE2 89.9 REMARK 620 3 HOH B 214 O 82.7 172.3 REMARK 620 4 HOH B 240 O 91.9 94.3 88.3 REMARK 620 5 HOH B 347 O 176.5 86.6 100.7 88.9 REMARK 620 6 HOH B 414 O 91.6 74.7 103.1 168.5 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 100 OE1 REMARK 620 2 GLU B 104 OE2 93.5 REMARK 620 3 GLU B 151 OE2 174.7 88.7 REMARK 620 4 HOH B 229 O 90.5 99.7 84.4 REMARK 620 5 HOH B 414 O 99.1 86.8 85.8 168.1 REMARK 620 6 HOH B 415 O 86.3 168.4 92.6 91.9 81.8 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 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 192 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O52 RELATED DB: PDB REMARK 900 E. COLI GDPMK IN COMPLEX WITH TARTRATE REMARK 900 RELATED ID: 3O69 RELATED DB: PDB REMARK 900 E. COLI GDPMK E100A MUTANT IN COMPLEX WITH MG++ REMARK 900 RELATED ID: 3O61 RELATED DB: PDB REMARK 900 E. COLI GDPMK E100A MUTANT IN COMPLEX WITH GDP-MANNOSE + MG++ DBREF 3O6Z A 1 191 UNP P37128 NUDK_ECOLI 1 191 DBREF 3O6Z B 1 191 UNP P37128 NUDK_ECOLI 1 191 SEQADV 3O6Z ALA A 152 UNP P37128 ASP 152 ENGINEERED MUTATION SEQADV 3O6Z ALA B 152 UNP P37128 ASP 152 ENGINEERED MUTATION SEQRES 1 A 191 MET THR GLN GLN ILE THR LEU ILE LYS ASP LYS ILE LEU SEQRES 2 A 191 SER ASP ASN TYR PHE THR LEU HIS ASN ILE THR TYR ASP SEQRES 3 A 191 LEU THR ARG LYS ASP GLY GLU VAL ILE ARG HIS LYS ARG SEQRES 4 A 191 GLU VAL TYR ASP ARG GLY ASN GLY ALA THR ILE LEU LEU SEQRES 5 A 191 TYR ASN THR LYS LYS LYS THR VAL VAL LEU ILE ARG GLN SEQRES 6 A 191 PHE ARG VAL ALA THR TRP VAL ASN GLY ASN GLU SER GLY SEQRES 7 A 191 GLN LEU ILE GLU SER CYS ALA GLY LEU LEU ASP ASN ASP SEQRES 8 A 191 GLU PRO GLU VAL CYS ILE ARG LYS GLU ALA ILE GLU GLU SEQRES 9 A 191 THR GLY TYR GLU VAL GLY GLU VAL ARG LYS LEU PHE GLU SEQRES 10 A 191 LEU TYR MET SER PRO GLY GLY VAL THR GLU LEU ILE HIS SEQRES 11 A 191 PHE PHE ILE ALA GLU TYR SER ASP ASN GLN ARG ALA ASN SEQRES 12 A 191 ALA GLY GLY GLY VAL GLU ASP GLU ALA ILE GLU VAL LEU SEQRES 13 A 191 GLU LEU PRO PHE SER GLN ALA LEU GLU MET ILE LYS THR SEQRES 14 A 191 GLY GLU ILE ARG ASP GLY LYS THR VAL LEU LEU LEU ASN SEQRES 15 A 191 TYR LEU GLN THR SER HIS LEU MET ASP SEQRES 1 B 191 MET THR GLN GLN ILE THR LEU ILE LYS ASP LYS ILE LEU SEQRES 2 B 191 SER ASP ASN TYR PHE THR LEU HIS ASN ILE THR TYR ASP SEQRES 3 B 191 LEU THR ARG LYS ASP GLY GLU VAL ILE ARG HIS LYS ARG SEQRES 4 B 191 GLU VAL TYR ASP ARG GLY ASN GLY ALA THR ILE LEU LEU SEQRES 5 B 191 TYR ASN THR LYS LYS LYS THR VAL VAL LEU ILE ARG GLN SEQRES 6 B 191 PHE ARG VAL ALA THR TRP VAL ASN GLY ASN GLU SER GLY SEQRES 7 B 191 GLN LEU ILE GLU SER CYS ALA GLY LEU LEU ASP ASN ASP SEQRES 8 B 191 GLU PRO GLU VAL CYS ILE ARG LYS GLU ALA ILE GLU GLU SEQRES 9 B 191 THR GLY TYR GLU VAL GLY GLU VAL ARG LYS LEU PHE GLU SEQRES 10 B 191 LEU TYR MET SER PRO GLY GLY VAL THR GLU LEU ILE HIS SEQRES 11 B 191 PHE PHE ILE ALA GLU TYR SER ASP ASN GLN ARG ALA ASN SEQRES 12 B 191 ALA GLY GLY GLY VAL GLU ASP GLU ALA ILE GLU VAL LEU SEQRES 13 B 191 GLU LEU PRO PHE SER GLN ALA LEU GLU MET ILE LYS THR SEQRES 14 B 191 GLY GLU ILE ARG ASP GLY LYS THR VAL LEU LEU LEU ASN SEQRES 15 B 191 TYR LEU GLN THR SER HIS LEU MET ASP HET MG A 202 1 HET MG B 201 1 HET MG B 202 1 HET CL B 204 1 HET CL B 203 1 HET PEG B 205 7 HET TRS B 206 8 HET PEG B 192 7 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 MG 3(MG 2+) FORMUL 6 CL 2(CL 1-) FORMUL 8 PEG 2(C4 H10 O3) FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 11 HOH *329(H2 O) HELIX 1 1 ARG A 67 VAL A 72 1 6 HELIX 2 2 GLU A 92 THR A 105 1 14 HELIX 3 3 PHE A 160 GLY A 170 1 11 HELIX 4 4 ASP A 174 HIS A 188 1 15 HELIX 5 5 ARG B 67 VAL B 72 1 6 HELIX 6 6 GLU B 92 GLY B 106 1 15 HELIX 7 7 SER B 137 ARG B 141 5 5 HELIX 8 8 PHE B 160 GLY B 170 1 11 HELIX 9 9 ASP B 174 HIS B 188 1 15 SHEET 1 A 3 ILE A 5 SER A 14 0 SHEET 2 A 3 THR A 19 THR A 28 -1 O LEU A 20 N LEU A 13 SHEET 3 A 3 VAL A 34 ASP A 43 -1 O ARG A 39 N ILE A 23 SHEET 1 B 5 GLN A 79 GLU A 82 0 SHEET 2 B 5 THR A 59 PHE A 66 -1 N ILE A 63 O GLU A 82 SHEET 3 B 5 GLY A 47 ASN A 54 -1 N ASN A 54 O THR A 59 SHEET 4 B 5 LEU A 128 GLU A 135 1 O HIS A 130 N GLY A 47 SHEET 5 B 5 VAL A 112 TYR A 119 -1 N ARG A 113 O ILE A 133 SHEET 1 C 4 CYS A 84 LEU A 87 0 SHEET 2 C 4 GLY A 47 ASN A 54 -1 N ALA A 48 O GLY A 86 SHEET 3 C 4 THR A 59 PHE A 66 -1 O THR A 59 N ASN A 54 SHEET 4 C 4 GLU A 154 PRO A 159 -1 O LEU A 156 N LEU A 62 SHEET 1 D 3 ILE B 5 ASP B 15 0 SHEET 2 D 3 THR B 19 LEU B 27 -1 O LEU B 20 N LEU B 13 SHEET 3 D 3 ILE B 35 ASP B 43 -1 O ASP B 43 N THR B 19 SHEET 1 E 5 GLN B 79 GLU B 82 0 SHEET 2 E 5 THR B 59 PHE B 66 -1 N ILE B 63 O GLU B 82 SHEET 3 E 5 GLY B 47 ASN B 54 -1 N ASN B 54 O THR B 59 SHEET 4 E 5 LEU B 128 GLU B 135 1 O HIS B 130 N GLY B 47 SHEET 5 E 5 ARG B 113 TYR B 119 -1 N ARG B 113 O ILE B 133 SHEET 1 F 4 CYS B 84 LEU B 87 0 SHEET 2 F 4 GLY B 47 ASN B 54 -1 N ILE B 50 O CYS B 84 SHEET 3 F 4 THR B 59 PHE B 66 -1 O THR B 59 N ASN B 54 SHEET 4 F 4 GLU B 154 PRO B 159 -1 O LEU B 156 N LEU B 62 LINK O ALA A 85 MG MG A 202 1555 1555 2.35 LINK OE2 GLU A 104 MG MG A 202 1555 1555 1.98 LINK MG MG A 202 O HOH A 311 1555 1555 2.18 LINK MG MG A 202 O HOH A 324 1555 1555 2.26 LINK MG MG A 202 O HOH A 417 1555 1555 1.91 LINK O ALA B 85 MG MG B 202 1555 1555 2.29 LINK OE1 GLU B 100 MG MG B 201 1555 1555 1.98 LINK OE2 GLU B 104 MG MG B 201 1555 1555 1.94 LINK OE2 GLU B 104 MG MG B 202 1555 1555 2.33 LINK OE2 GLU B 151 MG MG B 201 1555 1555 2.29 LINK MG MG B 201 O HOH B 229 1555 1555 2.31 LINK MG MG B 201 O HOH B 414 1555 1555 1.94 LINK MG MG B 201 O HOH B 415 1555 1555 2.21 LINK MG MG B 202 O HOH B 214 1555 1555 2.40 LINK MG MG B 202 O HOH B 240 1555 1555 2.21 LINK MG MG B 202 O HOH B 347 1555 1555 2.46 LINK MG MG B 202 O HOH B 414 1555 1555 2.06 SITE 1 AC1 5 ALA A 85 GLU A 104 HOH A 311 HOH A 324 SITE 2 AC1 5 HOH A 417 SITE 1 AC2 7 GLU B 100 GLU B 104 GLU B 151 MG B 202 SITE 2 AC2 7 HOH B 229 HOH B 414 HOH B 415 SITE 1 AC3 8 ALA B 85 GLU B 104 GLU B 151 MG B 201 SITE 2 AC3 8 HOH B 214 HOH B 240 HOH B 347 HOH B 414 SITE 1 AC4 1 ARG B 113 SITE 1 AC5 2 GLN B 4 THR B 28 SITE 1 AC6 5 GLU B 94 VAL B 95 LYS B 99 HOH B 327 SITE 2 AC6 5 HOH B 350 SITE 1 AC7 4 ARG B 64 ILE B 81 MET B 166 GLU B 171 SITE 1 AC8 6 ILE A 8 ARG A 36 ASP B 15 THR B 19 SITE 2 AC8 6 HIS B 21 ASP B 43 CRYST1 58.916 69.333 99.612 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016973 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014423 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010039 0.00000