HEADER HYDROLASE 16-MAY-14 4UME TITLE CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE TITLE 2 PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM ION TITLE 3 AND KDO MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE; COMPND 5 EC: 3.1.3.45; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MORAXELLA CATARRHALIS BC8; SOURCE 3 ORGANISM_TAXID: 857574; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28C KEYWDS HYDROLASE, HAD SUPERFAMILY EXPDTA X-RAY DIFFRACTION AUTHOR S.DHINDWAL,S.TOMAR,P.KUMAR REVDAT 4 10-JAN-24 4UME 1 HETSYN REVDAT 3 29-JUL-20 4UME 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 25-FEB-15 4UME 1 JRNL REVDAT 1 11-FEB-15 4UME 0 JRNL AUTH S.DHINDWAL,P.PRIYADARSHINI,D.N.PATIL,S.TAPAS,P.KUMAR, JRNL AUTH 2 S.TOMAR,P.KUMAR JRNL TITL LIGAND-BOUND STRUCTURES OF 3-DEOXY-D-MANNO-OCTULOSONATE JRNL TITL 2 8-PHOSPHATE PHOSPHATASE FROM MORAXELLA CATARRHALIS REVEAL A JRNL TITL 3 WATER CHANNEL CONNECTING TO THE ACTIVE SITE FOR THE SECOND JRNL TITL 4 STEP OF CATALYSIS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 239 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25664734 JRNL DOI 10.1107/S1399004714025218 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 8733 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 431 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) : 2.09 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 588 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 25 REMARK 3 BIN FREE R VALUE : 0.4060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1322 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.36 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) : 1.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.278 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.014 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1354 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1825 ; 1.259 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 173 ; 5.668 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;39.014 ;25.345 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 245 ;17.623 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;19.816 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 214 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 988 ; 0.004 ; 0.020 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): 695 ; 0.662 ; 1.798 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 867 ; 1.120 ; 2.691 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 659 ; 0.935 ; 1.992 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4UME COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : BRUKER AXS MICROSTAR-H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 43.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3N1U REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MG FORMATE, 100 MM BIS-TRIS REMARK 280 PROPANE (PH 5.0), 28% W/V PEG 3350, KDO, NA PHOSPHATE, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 43.30500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.30500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.70000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.30500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.30500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.70000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 43.30500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 43.30500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 20.70000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 43.30500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 43.30500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 20.70000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.1 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 A1176 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A1177 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A1178 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2025 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 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 115 CA - CB - CG ANGL. DEV. = 17.4 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 VAL A 18 -68.08 -94.27 REMARK 500 ASN A 148 18.22 -140.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2032 DISTANCE = 6.17 ANGSTROMS 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 A1175 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 17 OD2 REMARK 620 2 ASP A 19 O 95.6 REMARK 620 3 ASP A 110 OD1 90.5 89.3 REMARK 620 4 HOH A2006 O 87.6 84.9 173.6 REMARK 620 5 HOH A2007 O 91.0 172.4 86.8 99.2 REMARK 620 6 HOH A2009 O 174.2 81.8 84.4 97.3 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1176 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2085 O REMARK 620 2 HOH A2085 O 160.1 REMARK 620 3 HOH A2085 O 88.3 88.3 REMARK 620 4 HOH A2085 O 88.3 88.3 160.1 REMARK 620 5 HOH A2086 O 132.5 65.5 117.9 78.1 REMARK 620 6 HOH A2086 O 117.9 78.1 65.5 132.5 54.8 REMARK 620 7 HOH A2086 O 78.1 117.9 132.5 65.5 54.8 81.2 REMARK 620 8 HOH A2086 O 65.5 132.5 78.1 117.9 81.2 54.8 54.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1177 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2084 O REMARK 620 2 HOH A2084 O 71.3 REMARK 620 3 HOH A2084 O 48.7 48.7 REMARK 620 4 HOH A2084 O 48.7 48.7 71.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UM5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE REMARK 900 PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM REMARK 900 ION AND PHOSPHATE ION REMARK 900 RELATED ID: 4UM6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 11S GLOBULIN FROM WRIGHTIA TINCTORIA IN REMARK 900 COMPLEX WITH INDOLE-3-ACETYL-EPSILON- LYSINE CONJUGATE REMARK 900 RELATED ID: 4UM7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE REMARK 900 PHOSPHATASE (KDSC) FROM MORAXELLA CATARRHALIS IN COMPLEX WITH REMARK 900 MAGNESIUM ION REMARK 900 RELATED ID: 4UMD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE REMARK 900 PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 4UMF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 3-DEOXY-D-MANNO-OCTULOSONATE 8- PHOSPHATE REMARK 900 PHOSPHATASE FROM MORAXELLA CATARRHALIS IN COMPLEX WITH MAGNESIUM REMARK 900 ION, PHOSPHATE ION AND KDO MOLECULE DBREF 4UME A 1 173 UNP F1X4B5 F1X4B5_MORCA 1 173 SEQADV 4UME MET A -19 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME GLY A -18 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME SER A -17 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME SER A -16 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -15 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -14 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -13 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -12 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -11 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A -10 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME SER A -9 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME SER A -8 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME GLU A -7 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME ASN A -6 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME LEU A -5 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME TYR A -4 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME PHE A -3 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME GLN A -2 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME GLY A -1 UNP F1X4B5 EXPRESSION TAG SEQADV 4UME HIS A 0 UNP F1X4B5 EXPRESSION TAG SEQRES 1 A 193 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLU SEQRES 2 A 193 ASN LEU TYR PHE GLN GLY HIS MET ASN GLU ILE TYR GLN SEQRES 3 A 193 LYS ALA LYS HIS ILE LYS LEU PHE ALA MET ASP VAL ASP SEQRES 4 A 193 GLY ILE LEU SER ASP GLY GLN ILE ILE TYR ASN SER GLU SEQRES 5 A 193 GLY THR GLU THR LYS ALA PHE TYR VAL GLN ASP GLY LEU SEQRES 6 A 193 GLY LEU GLN ALA LEU LYS GLN SER GLY ILE ILE LEU ALA SEQRES 7 A 193 ILE ILE THR GLY ARG SER SER ALA MET VAL ASP ARG ARG SEQRES 8 A 193 ALA LYS GLU LEU GLY ILE SER HIS ILE ILE GLN GLY GLN SEQRES 9 A 193 ASP ASP LYS LEU THR ALA LEU VAL GLY LEU THR LYS LYS SEQRES 10 A 193 LEU GLY ILE GLU LEU SER HIS CYS ALA TYR ILE GLY ASP SEQRES 11 A 193 ASP LEU PRO ASP LEU LYS ALA VAL ARG GLU ALA GLY PHE SEQRES 12 A 193 GLY ILE SER VAL PRO ASN GLY CYS GLU GLN THR ARG ALA SEQRES 13 A 193 VAL SER ASP TYR ILE THR THR LYS THR GLY GLY ASN GLY SEQRES 14 A 193 ALA VAL ARG GLU VAL CYS GLU LEU ILE LEU LYS ALA GLN SEQRES 15 A 193 ASN ASN PHE ASP ALA PHE ILE ALA THR PHE GLN HET KDO A1174 16 HET MG A1175 1 HET MG A1176 1 HET MG A1177 1 HET MG A1178 1 HETNAM KDO 3-DEOXY-ALPHA-D-MANNO-OCT-2-ULOPYRANOSONIC ACID HETNAM MG MAGNESIUM ION HETSYN KDO 3-DEOXY-D-MANNO-OCT-2-ULOPYRANOSONIC ACID; 2-KETO-3- HETSYN 2 KDO DEOXY-D-MANNOOCTANOIC ACID; 3-DEOXY-ALPHA-D-MANNO-OCT- HETSYN 3 KDO 2-ULOSONIC ACID; 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID; HETSYN 4 KDO 3-DEOXY-MANNO-OCT-2-ULOSONIC ACID FORMUL 2 KDO C8 H14 O8 FORMUL 3 MG 4(MG 2+) FORMUL 7 HOH *86(H2 O) HELIX 1 1 MET A 1 LYS A 9 1 9 HELIX 2 2 TYR A 40 SER A 53 1 14 HELIX 3 3 SER A 65 GLY A 76 1 12 HELIX 4 4 ASP A 86 GLY A 99 1 14 HELIX 5 5 GLU A 101 SER A 103 5 3 HELIX 6 6 ASP A 111 PRO A 113 5 3 HELIX 7 7 ASP A 114 ALA A 121 1 8 HELIX 8 8 CYS A 131 VAL A 137 1 7 HELIX 9 9 GLY A 149 GLN A 162 1 14 HELIX 10 10 ASN A 164 THR A 171 1 8 SHEET 1 AA 6 HIS A 79 ILE A 81 0 SHEET 2 AA 6 ILE A 56 ILE A 60 1 O ILE A 59 N ILE A 81 SHEET 3 AA 6 LEU A 13 MET A 16 1 O PHE A 14 N ALA A 58 SHEET 4 AA 6 CYS A 105 ILE A 108 1 O ALA A 106 N ALA A 15 SHEET 5 AA 6 PHE A 123 SER A 126 1 O PHE A 123 N TYR A 107 SHEET 6 AA 6 TYR A 140 ILE A 141 1 O TYR A 140 N SER A 126 SHEET 1 AB 2 ILE A 28 TYR A 29 0 SHEET 2 AB 2 GLU A 35 THR A 36 -1 O THR A 36 N ILE A 28 LINK OD2 ASP A 17 MG MG A1175 1555 1555 1.96 LINK O ASP A 19 MG MG A1175 1555 1555 2.17 LINK OD1 ASP A 110 MG MG A1175 1555 1555 2.02 LINK MG MG A1175 O HOH A2006 1555 1555 2.08 LINK MG MG A1175 O HOH A2007 1555 1555 2.05 LINK MG MG A1175 O HOH A2009 1555 1555 2.07 LINK MG MG A1176 O HOH A2085 1555 4555 2.32 LINK MG MG A1176 O HOH A2085 1555 3555 2.32 LINK MG MG A1176 O HOH A2085 1555 2555 2.32 LINK MG MG A1176 O HOH A2085 1555 1555 2.32 LINK MG MG A1176 O HOH A2086 1555 1555 2.50 LINK MG MG A1176 O HOH A2086 1555 3555 2.50 LINK MG MG A1176 O HOH A2086 1555 4555 2.50 LINK MG MG A1176 O HOH A2086 1555 2555 2.50 LINK MG MG A1177 O HOH A2084 1555 3555 2.82 LINK MG MG A1177 O HOH A2084 1555 4555 2.82 LINK MG MG A1177 O HOH A2084 1555 2555 2.82 LINK MG MG A1177 O HOH A2084 1555 1555 2.82 CRYST1 86.610 86.610 41.400 90.00 90.00 90.00 I 4 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 0.011546 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024155 0.00000