HEADER HYDROLASE 06-JUL-09 3I6B TITLE CRYSTAL STRUCTURE OF YRBI LACKING THE LAST 8 RESIDUES, IN COMPLEX WITH TITLE 2 KDO AND INORGANIC PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 1-180; COMPND 5 SYNONYM: KDO 8-P PHOSPHATASE; COMPND 6 EC: 3.1.3.45; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 37762; SOURCE 4 STRAIN: B; SOURCE 5 GENE: C3958, KDSC, YRBI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS YRBI, KDSC, KDO, PHOSPHATASE, HYDROLASE, LIPOPOLYSACCHARIDE KEYWDS 2 BIOSYNTHESIS, MAGNESIUM EXPDTA X-RAY DIFFRACTION AUTHOR T.BISWAS,O.V.TSODIKOV REVDAT 5 06-SEP-23 3I6B 1 HETSYN REVDAT 4 29-JUL-20 3I6B 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 3I6B 1 VERSN REVDAT 2 03-NOV-09 3I6B 1 JRNL REVDAT 1 01-SEP-09 3I6B 0 JRNL AUTH T.BISWAS,L.YI,P.AGGARWAL,J.WU,J.R.RUBIN,J.A.STUCKEY, JRNL AUTH 2 R.W.WOODARD,O.V.TSODIKOV JRNL TITL THE TAIL OF KDSC: CONFORMATIONAL CHANGES CONTROL THE JRNL TITL 2 ACTIVITY OF A HALOACID DEHALOGENASE SUPERFAMILY PHOSPHATASE. JRNL REF J.BIOL.CHEM. V. 284 30594 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19726684 JRNL DOI 10.1074/JBC.M109.012278 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 21494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1132 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1600 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5198 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 188 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) : 24.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 1.17000 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): 0.312 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.225 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5310 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7213 ; 1.072 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 694 ; 4.855 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;32.421 ;24.400 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 903 ;14.727 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;17.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 879 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3858 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2496 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3643 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 298 ; 0.167 ; 0.200 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): 85 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.134 ; 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): 3534 ; 0.491 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5491 ; 0.633 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1976 ; 1.137 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1722 ; 1.799 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 179 REMARK 3 RESIDUE RANGE : B 900 B 900 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6515 -15.7209 -15.2979 REMARK 3 T TENSOR REMARK 3 T11: -0.0618 T22: -0.0382 REMARK 3 T33: -0.0875 T12: -0.0173 REMARK 3 T13: -0.0041 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 1.3460 L22: 1.8230 REMARK 3 L33: 1.0235 L12: -0.3956 REMARK 3 L13: 0.2963 L23: -0.3229 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.0301 S13: -0.0014 REMARK 3 S21: -0.0171 S22: -0.0128 S23: 0.0687 REMARK 3 S31: 0.0080 S32: -0.0539 S33: -0.0030 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 : B 6 B 180 REMARK 3 ORIGIN FOR THE GROUP (A): 44.2419 -14.6004 -20.9276 REMARK 3 T TENSOR REMARK 3 T11: -0.1168 T22: -0.0150 REMARK 3 T33: -0.0302 T12: 0.0197 REMARK 3 T13: -0.0001 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.8691 L22: 2.3320 REMARK 3 L33: 2.0183 L12: 0.7163 REMARK 3 L13: -0.4393 L23: -0.2410 REMARK 3 S TENSOR REMARK 3 S11: 0.0207 S12: 0.0673 S13: -0.1499 REMARK 3 S21: -0.1094 S22: -0.0169 S23: -0.0978 REMARK 3 S31: 0.0472 S32: 0.0971 S33: -0.0038 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 6 C 180 REMARK 3 RESIDUE RANGE : D 900 D 900 REMARK 3 ORIGIN FOR THE GROUP (A): 49.5177 -20.0769 8.9744 REMARK 3 T TENSOR REMARK 3 T11: -0.0779 T22: -0.0639 REMARK 3 T33: -0.0780 T12: 0.0061 REMARK 3 T13: 0.0024 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.2160 L22: 1.6736 REMARK 3 L33: 1.1647 L12: -0.2900 REMARK 3 L13: 0.3624 L23: 0.3618 REMARK 3 S TENSOR REMARK 3 S11: -0.0460 S12: -0.0742 S13: -0.0275 REMARK 3 S21: -0.0053 S22: 0.0321 S23: -0.1550 REMARK 3 S31: 0.0073 S32: 0.0168 S33: 0.0139 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 6 D 180 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0058 -20.9146 14.6451 REMARK 3 T TENSOR REMARK 3 T11: -0.0763 T22: -0.0199 REMARK 3 T33: -0.0358 T12: -0.0140 REMARK 3 T13: -0.0043 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.7694 L22: 1.8262 REMARK 3 L33: 1.3514 L12: -0.3574 REMARK 3 L13: -0.5359 L23: 0.5594 REMARK 3 S TENSOR REMARK 3 S11: -0.0117 S12: -0.0121 S13: -0.1045 REMARK 3 S21: 0.0780 S22: -0.0131 S23: 0.0901 REMARK 3 S31: 0.0806 S32: -0.0162 S33: 0.0248 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 3I6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.06699 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB CODE: 2R8E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.875 M AMMONIUM SULFATE, 100MM NA REMARK 280 CACODYLATE PH 6.5, 2.5% GLYCEROL, STOICHIOMETRIC AMOUNT OF KDO8P REMARK 280 (CLEAVED UPON INCUBATION IN THE DROP), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.92700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.92700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 32.48200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.05200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.48200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.05200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.92700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.48200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.05200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.92700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.48200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.05200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 10390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -248.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 2 REMARK 465 LYS A 3 REMARK 465 ALA A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 180 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 LYS B 3 REMARK 465 ALA B 4 REMARK 465 GLY B 5 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 LYS C 3 REMARK 465 ALA C 4 REMARK 465 GLY C 5 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 LYS D 3 REMARK 465 ALA D 4 REMARK 465 GLY D 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 69 CG OD1 OD2 REMARK 470 ARG B 78 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 69 CG OD1 OD2 REMARK 470 ASP D 69 CG OD1 OD2 REMARK 470 ARG D 78 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 111 CG CD OE1 OE2 REMARK 470 GLU D 118 CG CD OE1 OE2 REMARK 470 GLU D 134 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 125 NH2 ARG B 57 1.81 REMARK 500 NH1 ARG C 78 O5 KDO D 900 1.83 REMARK 500 CA GLY D 59 O1B KDO D 900 1.99 REMARK 500 CG ARG A 78 O5 KDO B 900 2.11 REMARK 500 N GLY D 59 O1B KDO D 900 2.16 REMARK 500 O4 PO4 A 800 O8 KDO B 900 2.19 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 33 -74.09 -86.67 REMARK 500 VAL B 36 -72.83 -113.76 REMARK 500 VAL C 33 -66.78 -92.75 REMARK 500 VAL C 36 -59.94 -122.06 REMARK 500 VAL D 33 -72.48 -83.70 REMARK 500 ASP D 125 -8.36 -146.44 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 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 34 O REMARK 620 2 PO4 A 800 O1 99.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 34 O REMARK 620 2 ASP C 125 OD1 86.9 REMARK 620 3 PO4 C 800 O3 80.5 152.9 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2R8X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 2R8Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN A REMARK 900 COMPLEX WITH CA REMARK 900 RELATED ID: 2R8Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN REMARK 900 COMPLEX WITH A PHOSPHATE AND A CALCIUM ION REMARK 900 RELATED ID: 2R8E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF YRBI FROM ESCHERICHIA COLI IN COMPLEX WITH MG REMARK 900 RELATED ID: 3HYC RELATED DB: PDB DBREF 3I6B A 1 180 UNP P67653 KDSC_ECOL6 1 180 DBREF 3I6B B 1 180 UNP P67653 KDSC_ECOL6 1 180 DBREF 3I6B C 1 180 UNP P67653 KDSC_ECOL6 1 180 DBREF 3I6B D 1 180 UNP P67653 KDSC_ECOL6 1 180 SEQRES 1 A 180 MET SER LYS ALA GLY ALA SER LEU ALA THR CYS TYR GLY SEQRES 2 A 180 PRO VAL SER ALA ASP VAL MET ALA LYS ALA GLU ASN ILE SEQRES 3 A 180 ARG LEU LEU ILE LEU ASP VAL ASP GLY VAL LEU SER ASP SEQRES 4 A 180 GLY LEU ILE TYR MET GLY ASN ASN GLY GLU GLU LEU LYS SEQRES 5 A 180 ALA PHE ASN VAL ARG ASP GLY TYR GLY ILE ARG CYS ALA SEQRES 6 A 180 LEU THR SER ASP ILE GLU VAL ALA ILE ILE THR GLY ARG SEQRES 7 A 180 LYS ALA LYS LEU VAL GLU ASP ARG CYS ALA THR LEU GLY SEQRES 8 A 180 ILE THR HIS LEU TYR GLN GLY GLN SER ASN LYS LEU ILE SEQRES 9 A 180 ALA PHE SER ASP LEU LEU GLU LYS LEU ALA ILE ALA PRO SEQRES 10 A 180 GLU ASN VAL ALA TYR VAL GLY ASP ASP LEU ILE ASP TRP SEQRES 11 A 180 PRO VAL MET GLU LYS VAL GLY LEU SER VAL ALA VAL ALA SEQRES 12 A 180 ASP ALA HIS PRO LEU LEU ILE PRO ARG ALA ASP TYR VAL SEQRES 13 A 180 THR ARG ILE ALA GLY GLY ARG GLY ALA VAL ARG GLU VAL SEQRES 14 A 180 CYS ASP LEU LEU LEU LEU ALA GLN GLY LYS LEU SEQRES 1 B 180 MET SER LYS ALA GLY ALA SER LEU ALA THR CYS TYR GLY SEQRES 2 B 180 PRO VAL SER ALA ASP VAL MET ALA LYS ALA GLU ASN ILE SEQRES 3 B 180 ARG LEU LEU ILE LEU ASP VAL ASP GLY VAL LEU SER ASP SEQRES 4 B 180 GLY LEU ILE TYR MET GLY ASN ASN GLY GLU GLU LEU LYS SEQRES 5 B 180 ALA PHE ASN VAL ARG ASP GLY TYR GLY ILE ARG CYS ALA SEQRES 6 B 180 LEU THR SER ASP ILE GLU VAL ALA ILE ILE THR GLY ARG SEQRES 7 B 180 LYS ALA LYS LEU VAL GLU ASP ARG CYS ALA THR LEU GLY SEQRES 8 B 180 ILE THR HIS LEU TYR GLN GLY GLN SER ASN LYS LEU ILE SEQRES 9 B 180 ALA PHE SER ASP LEU LEU GLU LYS LEU ALA ILE ALA PRO SEQRES 10 B 180 GLU ASN VAL ALA TYR VAL GLY ASP ASP LEU ILE ASP TRP SEQRES 11 B 180 PRO VAL MET GLU LYS VAL GLY LEU SER VAL ALA VAL ALA SEQRES 12 B 180 ASP ALA HIS PRO LEU LEU ILE PRO ARG ALA ASP TYR VAL SEQRES 13 B 180 THR ARG ILE ALA GLY GLY ARG GLY ALA VAL ARG GLU VAL SEQRES 14 B 180 CYS ASP LEU LEU LEU LEU ALA GLN GLY LYS LEU SEQRES 1 C 180 MET SER LYS ALA GLY ALA SER LEU ALA THR CYS TYR GLY SEQRES 2 C 180 PRO VAL SER ALA ASP VAL MET ALA LYS ALA GLU ASN ILE SEQRES 3 C 180 ARG LEU LEU ILE LEU ASP VAL ASP GLY VAL LEU SER ASP SEQRES 4 C 180 GLY LEU ILE TYR MET GLY ASN ASN GLY GLU GLU LEU LYS SEQRES 5 C 180 ALA PHE ASN VAL ARG ASP GLY TYR GLY ILE ARG CYS ALA SEQRES 6 C 180 LEU THR SER ASP ILE GLU VAL ALA ILE ILE THR GLY ARG SEQRES 7 C 180 LYS ALA LYS LEU VAL GLU ASP ARG CYS ALA THR LEU GLY SEQRES 8 C 180 ILE THR HIS LEU TYR GLN GLY GLN SER ASN LYS LEU ILE SEQRES 9 C 180 ALA PHE SER ASP LEU LEU GLU LYS LEU ALA ILE ALA PRO SEQRES 10 C 180 GLU ASN VAL ALA TYR VAL GLY ASP ASP LEU ILE ASP TRP SEQRES 11 C 180 PRO VAL MET GLU LYS VAL GLY LEU SER VAL ALA VAL ALA SEQRES 12 C 180 ASP ALA HIS PRO LEU LEU ILE PRO ARG ALA ASP TYR VAL SEQRES 13 C 180 THR ARG ILE ALA GLY GLY ARG GLY ALA VAL ARG GLU VAL SEQRES 14 C 180 CYS ASP LEU LEU LEU LEU ALA GLN GLY LYS LEU SEQRES 1 D 180 MET SER LYS ALA GLY ALA SER LEU ALA THR CYS TYR GLY SEQRES 2 D 180 PRO VAL SER ALA ASP VAL MET ALA LYS ALA GLU ASN ILE SEQRES 3 D 180 ARG LEU LEU ILE LEU ASP VAL ASP GLY VAL LEU SER ASP SEQRES 4 D 180 GLY LEU ILE TYR MET GLY ASN ASN GLY GLU GLU LEU LYS SEQRES 5 D 180 ALA PHE ASN VAL ARG ASP GLY TYR GLY ILE ARG CYS ALA SEQRES 6 D 180 LEU THR SER ASP ILE GLU VAL ALA ILE ILE THR GLY ARG SEQRES 7 D 180 LYS ALA LYS LEU VAL GLU ASP ARG CYS ALA THR LEU GLY SEQRES 8 D 180 ILE THR HIS LEU TYR GLN GLY GLN SER ASN LYS LEU ILE SEQRES 9 D 180 ALA PHE SER ASP LEU LEU GLU LYS LEU ALA ILE ALA PRO SEQRES 10 D 180 GLU ASN VAL ALA TYR VAL GLY ASP ASP LEU ILE ASP TRP SEQRES 11 D 180 PRO VAL MET GLU LYS VAL GLY LEU SER VAL ALA VAL ALA SEQRES 12 D 180 ASP ALA HIS PRO LEU LEU ILE PRO ARG ALA ASP TYR VAL SEQRES 13 D 180 THR ARG ILE ALA GLY GLY ARG GLY ALA VAL ARG GLU VAL SEQRES 14 D 180 CYS ASP LEU LEU LEU LEU ALA GLN GLY LYS LEU HET MG A 201 1 HET PO4 A 800 5 HET MG B 202 1 HET PO4 B 800 5 HET KDO B 900 16 HET MG C 204 1 HET PO4 C 800 5 HET MG D 203 1 HET PO4 D 800 5 HET KDO D 900 16 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM KDO 3-DEOXY-ALPHA-D-MANNO-OCT-2-ULOPYRANOSONIC ACID 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 5 MG 4(MG 2+) FORMUL 6 PO4 4(O4 P 3-) FORMUL 9 KDO 2(C8 H14 O8) FORMUL 15 HOH *188(H2 O) HELIX 1 1 SER A 16 ASN A 25 1 10 HELIX 2 2 VAL A 56 THR A 67 1 12 HELIX 3 3 ALA A 80 GLY A 91 1 12 HELIX 4 4 ASN A 101 ALA A 114 1 14 HELIX 5 5 ALA A 116 GLU A 118 5 3 HELIX 6 6 ASP A 126 ILE A 128 5 3 HELIX 7 7 ASP A 129 GLU A 134 1 6 HELIX 8 8 LEU A 149 ALA A 153 5 5 HELIX 9 9 GLY A 164 GLN A 177 1 14 HELIX 10 10 ALA B 17 ASN B 25 1 9 HELIX 11 11 VAL B 56 SER B 68 1 13 HELIX 12 12 ALA B 80 GLY B 91 1 12 HELIX 13 13 ASN B 101 ALA B 114 1 14 HELIX 14 14 ALA B 116 GLU B 118 5 3 HELIX 15 15 ASP B 126 ILE B 128 5 3 HELIX 16 16 ASP B 129 GLU B 134 1 6 HELIX 17 17 LEU B 149 ALA B 153 5 5 HELIX 18 18 GLY B 164 GLN B 177 1 14 HELIX 19 19 ALA C 17 ASN C 25 1 9 HELIX 20 20 VAL C 56 THR C 67 1 12 HELIX 21 21 ALA C 80 GLY C 91 1 12 HELIX 22 22 LYS C 102 LEU C 113 1 12 HELIX 23 23 ALA C 116 GLU C 118 5 3 HELIX 24 24 ASP C 126 ILE C 128 5 3 HELIX 25 25 ASP C 129 GLU C 134 1 6 HELIX 26 26 LEU C 149 ALA C 153 5 5 HELIX 27 27 GLY C 164 GLN C 177 1 14 HELIX 28 28 ALA D 17 GLU D 24 1 8 HELIX 29 29 VAL D 56 SER D 68 1 13 HELIX 30 30 ALA D 80 GLY D 91 1 12 HELIX 31 31 ASN D 101 ALA D 114 1 14 HELIX 32 32 ALA D 116 GLU D 118 5 3 HELIX 33 33 ASP D 126 ILE D 128 5 3 HELIX 34 34 ASP D 129 GLU D 134 1 6 HELIX 35 35 LEU D 149 ALA D 153 5 5 HELIX 36 36 GLY D 164 GLN D 177 1 14 SHEET 1 A 6 HIS A 94 TYR A 96 0 SHEET 2 A 6 GLU A 71 ILE A 75 1 N ILE A 74 O TYR A 96 SHEET 3 A 6 LEU A 28 LEU A 31 1 N LEU A 29 O GLU A 71 SHEET 4 A 6 VAL A 120 GLY A 124 1 O ALA A 121 N ILE A 30 SHEET 5 A 6 LEU A 138 ALA A 141 1 O VAL A 140 N GLY A 124 SHEET 6 A 6 TYR A 155 VAL A 156 1 O TYR A 155 N ALA A 141 SHEET 1 B 9 LEU A 41 GLY A 45 0 SHEET 2 B 9 GLU A 50 ASN A 55 -1 O LEU A 51 N TYR A 43 SHEET 3 B 9 LEU D 41 GLY D 45 -1 O ILE D 42 N PHE A 54 SHEET 4 B 9 GLU D 50 ASN D 55 -1 O LEU D 51 N TYR D 43 SHEET 5 B 9 LEU C 41 GLY C 45 -1 N ILE C 42 O PHE D 54 SHEET 6 B 9 GLU C 50 ASN C 55 -1 O LEU C 51 N TYR C 43 SHEET 7 B 9 LEU B 41 GLY B 45 -1 N MET B 44 O LYS C 52 SHEET 8 B 9 GLU B 50 ASN B 55 -1 O LEU B 51 N TYR B 43 SHEET 9 B 9 LEU A 41 GLY A 45 -1 N MET A 44 O LYS B 52 SHEET 1 C 2 SER B 7 LEU B 8 0 SHEET 2 C 2 VAL B 15 SER B 16 -1 O VAL B 15 N LEU B 8 SHEET 1 D 6 HIS B 94 TYR B 96 0 SHEET 2 D 6 GLU B 71 ILE B 75 1 N ILE B 74 O TYR B 96 SHEET 3 D 6 LEU B 28 LEU B 31 1 N LEU B 29 O ALA B 73 SHEET 4 D 6 VAL B 120 GLY B 124 1 O ALA B 121 N ILE B 30 SHEET 5 D 6 LEU B 138 ALA B 141 1 O VAL B 140 N TYR B 122 SHEET 6 D 6 TYR B 155 VAL B 156 1 O TYR B 155 N ALA B 141 SHEET 1 E 2 SER C 7 LEU C 8 0 SHEET 2 E 2 VAL C 15 SER C 16 -1 O VAL C 15 N LEU C 8 SHEET 1 F 6 HIS C 94 TYR C 96 0 SHEET 2 F 6 GLU C 71 ILE C 75 1 N ILE C 74 O HIS C 94 SHEET 3 F 6 LEU C 28 LEU C 31 1 N LEU C 29 O GLU C 71 SHEET 4 F 6 VAL C 120 GLY C 124 1 O ALA C 121 N ILE C 30 SHEET 5 F 6 LEU C 138 ALA C 141 1 O VAL C 140 N TYR C 122 SHEET 6 F 6 TYR C 155 VAL C 156 1 O TYR C 155 N ALA C 141 SHEET 1 G 2 SER D 7 LEU D 8 0 SHEET 2 G 2 VAL D 15 SER D 16 -1 O VAL D 15 N LEU D 8 SHEET 1 H 6 HIS D 94 TYR D 96 0 SHEET 2 H 6 GLU D 71 ILE D 75 1 N ILE D 74 O TYR D 96 SHEET 3 H 6 LEU D 28 LEU D 31 1 N LEU D 29 O ALA D 73 SHEET 4 H 6 VAL D 120 GLY D 124 1 O ALA D 121 N ILE D 30 SHEET 5 H 6 LEU D 138 ALA D 141 1 O VAL D 140 N TYR D 122 SHEET 6 H 6 TYR D 155 VAL D 156 1 O TYR D 155 N ALA D 141 LINK O ASP A 34 MG MG A 201 1555 1555 2.40 LINK MG MG A 201 O1 PO4 A 800 1555 1555 2.29 LINK O ASP C 34 MG MG C 204 1555 1555 2.48 LINK OD1 ASP C 125 MG MG C 204 1555 1555 2.21 LINK MG MG C 204 O3 PO4 C 800 1555 1555 2.16 LINK MG MG D 203 O2 PO4 D 800 1555 1555 2.25 CRYST1 64.964 144.104 145.854 90.00 90.00 90.00 C 2 2 21 32 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 0.015393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006856 0.00000