HEADER HYDROLASE 16-JAN-14 4CML
TITLE CRYSTAL STRUCTURE OF INPP5B IN COMPLEX WITH PHOSPHATIDYLINOSITOL 3,4-
TITLE 2 BISPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE,
COMPND 3 ISOFORM 2;
COMPND 4 CHAIN: A;
COMPND 5 FRAGMENT: 5-PHOSPHATASE CATALYTIC DOMAIN, RESIDUES 259-563;
COMPND 6 SYNONYM: 75 KDA INOSITOL POLYPHOSPHATE-5-PHOSPHATASE,
COMPND 7 PHOSPHOINOSITIDE 5-PHOSPHATASE, 5PTASE;
COMPND 8 EC: 3.1.3.36;
COMPND 9 ENGINEERED: YES;
COMPND 10 OTHER_DETAILS: DOMAIN ENCOMPASSING RESIDUES 259 TO 563. CLONED WITH A
COMPND 11 C-TERMINAL HEXAHISTIDINE TAG.
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3 PRARE;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-CH2;
SOURCE 11 OTHER_DETAILS: MAMMALIAN GENE COLLECTION
KEYWDS HYDROLASE, SGC, SIGNALLING, STRUCTURAL GENOMICS CONSORTIUM STOCKHOLM,
KEYWDS 2 MAGNESIUM BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR L.TRESAUGUES,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,A.M.EDWARDS,
AUTHOR 2 T.EKBLAD,S.FLODIN,S.GRASLUND,T.KARLBERG,M.MOCHE,T.NYMAN,H.SCHULER,
AUTHOR 3 C.SILVANDER,A.G.THORSELL,J.WEIGELT,M.WELIN,P.NORDLUND
REVDAT 4 20-DEC-23 4CML 1 REMARK LINK
REVDAT 3 17-JAN-18 4CML 1 REMARK
REVDAT 2 21-MAY-14 4CML 1 JRNL
REVDAT 1 16-APR-14 4CML 0
JRNL AUTH L.TRESAUGUES,C.SILVANDER,S.FLODIN,M.WELIN,T.NYMAN,
JRNL AUTH 2 S.GRASLUND,M.HAMMARSTROM,H.BERGLUND,P.NORDLUND
JRNL TITL STRUCTURAL BASIS FOR PHOSPHOINOSITIDE SUBSTRATE RECOGNITION,
JRNL TITL 2 CATALYSIS, AND MEMBRANE INTERACTIONS IN HUMAN INOSITOL
JRNL TITL 3 POLYPHOSPHATE 5-PHOSPHATASES.
JRNL REF STRUCTURE V. 22 744 2014
JRNL REFN ISSN 0969-2126
JRNL PMID 24704254
JRNL DOI 10.1016/J.STR.2014.01.013
REMARK 2
REMARK 2 RESOLUTION. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 33778
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) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.199
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1786
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) : 2.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2473
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 BIN R VALUE (WORKING SET) : 0.3290
REMARK 3 BIN FREE R VALUE SET COUNT : 113
REMARK 3 BIN FREE R VALUE : 0.3730
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2496
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 60
REMARK 3 SOLVENT ATOMS : 320
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.57
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.148
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.189
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2633 ; 0.008 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 1764 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3573 ; 1.243 ; 1.956
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4298 ; 0.780 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 6.342 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;32.824 ;24.341
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;13.001 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.679 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 381 ; 0.076 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2899 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 543 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1551 ; 0.436 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 629 ; 0.090 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2507 ; 0.861 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1082 ; 1.422 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1065 ; 2.351 ; 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 : 2
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 258 A 421
REMARK 3 ORIGIN FOR THE GROUP (A): 6.2339 27.9053 -46.2963
REMARK 3 T TENSOR
REMARK 3 T11: 0.0828 T22: 0.0109
REMARK 3 T33: 0.0397 T12: -0.0025
REMARK 3 T13: 0.0229 T23: -0.0121
REMARK 3 L TENSOR
REMARK 3 L11: 4.2039 L22: 1.0071
REMARK 3 L33: 1.1095 L12: 0.6105
REMARK 3 L13: 0.1700 L23: 0.1558
REMARK 3 S TENSOR
REMARK 3 S11: 0.0492 S12: 0.0667 S13: 0.0507
REMARK 3 S21: 0.0294 S22: -0.0596 S23: 0.0127
REMARK 3 S31: -0.1080 S32: -0.0043 S33: 0.0104
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 422 A 567
REMARK 3 ORIGIN FOR THE GROUP (A): 7.4859 14.9150 -43.1725
REMARK 3 T TENSOR
REMARK 3 T11: 0.0770 T22: 0.0271
REMARK 3 T33: 0.1053 T12: -0.0207
REMARK 3 T13: 0.0136 T23: -0.0010
REMARK 3 L TENSOR
REMARK 3 L11: 4.2792 L22: 2.0124
REMARK 3 L33: 1.7491 L12: -0.5020
REMARK 3 L13: -0.2917 L23: -0.2234
REMARK 3 S TENSOR
REMARK 3 S11: -0.0558 S12: -0.1781 S13: -0.4480
REMARK 3 S21: 0.1637 S22: 0.0146 S23: -0.1148
REMARK 3 S31: 0.1143 S32: 0.0844 S33: 0.0412
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. U VALUES WITH TLS ADDED.
REMARK 4
REMARK 4 4CML COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JAN-14.
REMARK 100 THE DEPOSITION ID IS D_1290059481.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-APR-10
REMARK 200 TEMPERATURE (KELVIN) : 77
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : MAX II
REMARK 200 BEAMLINE : I911-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.037960
REMARK 200 MONOCHROMATOR : BENT SI (111) CRYSTAL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35595
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
REMARK 200 RESOLUTION RANGE LOW (A) : 29.890
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 5.500
REMARK 200 R MERGE (I) : 0.09000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 5.60
REMARK 200 R MERGE FOR SHELL (I) : 0.65000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 3N9V
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 77.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.58
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M NA-MALONATE PH 7.0, 0.1 M HEPES
REMARK 280 PH 7.0, 0.5% JEFFAMINE ED-2001 PH 7.0, 2MM MGSO4, 2MM PTDINS-(3,
REMARK 280 4,5)-P3 (1,2-DIOCTANOYL)
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3
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 5555 Z,X,Y
REMARK 290 6555 Z+1/2,-X+1/2,-Y
REMARK 290 7555 -Z+1/2,-X,Y+1/2
REMARK 290 8555 -Z,X+1/2,-Y+1/2
REMARK 290 9555 Y,Z,X
REMARK 290 10555 -Y,Z+1/2,-X+1/2
REMARK 290 11555 Y+1/2,-Z+1/2,-X
REMARK 290 12555 -Y+1/2,-Z,X+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 66.83050
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.83050
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.83050
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.83050
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.83050
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.83050
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 66.83050
REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 66.83050
REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 66.83050
REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 66.83050
REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 66.83050
REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 66.83050
REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 66.83050
REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 66.83050
REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 66.83050
REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 66.83050
REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 66.83050
REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 66.83050
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: 4170 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 39380 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.7 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 66.83050
REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 -66.83050
REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 66.83050
REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 66.83050
REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 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 HIS A 568
REMARK 465 HIS A 569
REMARK 465 HIS A 570
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 LYS A 324 CD CE NZ
REMARK 470 LYS A 335 CD CE NZ
REMARK 470 LYS A 416 CG CD CE NZ
REMARK 470 LYS A 462 CE NZ
REMARK 470 LYS A 467 NZ
REMARK 470 GLN A 470 CD OE1 NE2
REMARK 470 GLU A 515 CG CD OE1 OE2
REMARK 470 LYS A 529 NZ
REMARK 470 LYS A 531 NZ
REMARK 470 LYS A 545 NZ
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 NE2 GLN A 539 O HOH A 2297 2.16
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 SER A 288 60.07 -151.40
REMARK 500 PHE A 313 19.51 80.06
REMARK 500 VAL A 345 -108.56 54.47
REMARK 500 HIS A 390 -120.07 49.12
REMARK 500 HIS A 404 139.50 88.77
REMARK 500 PRO A 429 93.88 -62.17
REMARK 500 SER A 430 -46.92 170.80
REMARK 500 GLU A 454 -55.45 68.14
REMARK 500 ASP A 512 110.42 -27.40
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 A2118 DISTANCE = 7.46 ANGSTROMS
REMARK 525 HOH A2153 DISTANCE = 7.20 ANGSTROMS
REMARK 525 HOH A2318 DISTANCE = 9.06 ANGSTROMS
REMARK 525 HOH A2319 DISTANCE = 8.28 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 A1569 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 275 OD1
REMARK 620 2 GLU A 303 OE1 105.9
REMARK 620 3 HOH A2018 O 94.1 84.4
REMARK 620 4 HOH A2020 O 90.0 162.1 86.4
REMARK 620 5 HOH A2023 O 91.3 103.2 169.2 84.2
REMARK 620 6 HOH A2050 O 167.3 81.5 96.8 84.3 76.9
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 52N A 1568
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1569
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1570
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1571
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1572
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4CMN RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF OCRL IN COMPLEX WITH A PHOSPHATE ION
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 A HEXAHISTIDINE TAG AND AN EXTRA ALANINE WERE ADDED IN C-
REMARK 999 TERMINUS.
DBREF 4CML A 259 563 UNP P32019 I5P2_HUMAN 339 643
SEQADV 4CML MET A 258 UNP P32019 EXPRESSION TAG
SEQADV 4CML ALA A 564 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 565 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 566 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 567 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 568 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 569 UNP P32019 EXPRESSION TAG
SEQADV 4CML HIS A 570 UNP P32019 EXPRESSION TAG
SEQRES 1 A 313 MET TYR THR TYR ILE GLN ASN PHE ARG PHE PHE ALA GLY
SEQRES 2 A 313 THR TYR ASN VAL ASN GLY GLN SER PRO LYS GLU CYS LEU
SEQRES 3 A 313 ARG LEU TRP LEU SER ASN GLY ILE GLN ALA PRO ASP VAL
SEQRES 4 A 313 TYR CYS VAL GLY PHE GLN GLU LEU ASP LEU SER LYS GLU
SEQRES 5 A 313 ALA PHE PHE PHE HIS ASP THR PRO LYS GLU GLU GLU TRP
SEQRES 6 A 313 PHE LYS ALA VAL SER GLU GLY LEU HIS PRO ASP ALA LYS
SEQRES 7 A 313 TYR ALA LYS VAL LYS LEU ILE ARG LEU VAL GLY ILE MET
SEQRES 8 A 313 LEU LEU LEU TYR VAL LYS GLN GLU HIS ALA ALA TYR ILE
SEQRES 9 A 313 SER GLU VAL GLU ALA GLU THR VAL GLY THR GLY ILE MET
SEQRES 10 A 313 GLY ARG MET GLY ASN LYS GLY GLY VAL ALA ILE ARG PHE
SEQRES 11 A 313 GLN PHE HIS ASN THR SER ILE CYS VAL VAL ASN SER HIS
SEQRES 12 A 313 LEU ALA ALA HIS ILE GLU GLU TYR GLU ARG ARG ASN GLN
SEQRES 13 A 313 ASP TYR LYS ASP ILE CYS SER ARG MET GLN PHE CYS GLN
SEQRES 14 A 313 PRO ASP PRO SER LEU PRO PRO LEU THR ILE SER ASN HIS
SEQRES 15 A 313 ASP VAL ILE LEU TRP LEU GLY ASP LEU ASN TYR ARG ILE
SEQRES 16 A 313 GLU GLU LEU ASP VAL GLU LYS VAL LYS LYS LEU ILE GLU
SEQRES 17 A 313 GLU LYS ASP PHE GLN MET LEU TYR ALA TYR ASP GLN LEU
SEQRES 18 A 313 LYS ILE GLN VAL ALA ALA LYS THR VAL PHE GLU GLY PHE
SEQRES 19 A 313 THR GLU GLY GLU LEU THR PHE GLN PRO THR TYR LYS TYR
SEQRES 20 A 313 ASP THR GLY SER ASP ASP TRP ASP THR SER GLU LYS CYS
SEQRES 21 A 313 ARG ALA PRO ALA TRP CYS ASP ARG ILE LEU TRP LYS GLY
SEQRES 22 A 313 LYS ASN ILE THR GLN LEU SER TYR GLN SER HIS MET ALA
SEQRES 23 A 313 LEU LYS THR SER ASP HIS LYS PRO VAL SER SER VAL PHE
SEQRES 24 A 313 ASP ILE GLY VAL ARG VAL VAL ALA HIS HIS HIS HIS HIS
SEQRES 25 A 313 HIS
HET 52N A1568 47
HET MG A1569 1
HET CL A1570 1
HET SO4 A1571 5
HET GOL A1572 6
HETNAM 52N 1,2-DIOCTANOYL PHOSPHATIDYL EPI-INOSITOL (3,4)-
HETNAM 2 52N BISPHOSPHATE
HETNAM MG MAGNESIUM ION
HETNAM CL CHLORIDE ION
HETNAM SO4 SULFATE ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 52N C25 H49 O19 P3
FORMUL 3 MG MG 2+
FORMUL 4 CL CL 1-
FORMUL 5 SO4 O4 S 2-
FORMUL 6 GOL C3 H8 O3
FORMUL 7 HOH *320(H2 O)
HELIX 1 1 LEU A 283 SER A 288 1 6
HELIX 2 2 SER A 307 PHE A 312 1 6
HELIX 3 3 THR A 316 LEU A 330 1 15
HELIX 4 4 GLU A 356 ALA A 359 5 4
HELIX 5 5 GLY A 372 ARG A 376 5 5
HELIX 6 6 HIS A 404 GLU A 406 5 3
HELIX 7 7 GLU A 407 MET A 422 1 16
HELIX 8 8 ASP A 456 GLU A 466 1 11
HELIX 9 9 ASP A 468 ALA A 474 1 7
HELIX 10 10 ASP A 476 ALA A 484 1 9
SHEET 1 AA 6 TYR A 336 LEU A 344 0
SHEET 2 AA 6 ILE A 347 LYS A 354 -1 O ILE A 347 N LEU A 344
SHEET 3 AA 6 VAL A 296 GLN A 302 -1 O TYR A 297 N TYR A 352
SHEET 4 AA 6 THR A 260 ASN A 273 1 O PHE A 268 N CYS A 298
SHEET 5 AA 6 VAL A 552 VAL A 563 -1 O VAL A 552 N THR A 271
SHEET 6 AA 6 ILE A 533 SER A 540 -1 O THR A 534 N ASP A 557
SHEET 1 AB 5 ILE A 361 GLY A 370 0
SHEET 2 AB 5 GLY A 381 PHE A 389 -1 O GLY A 382 N VAL A 369
SHEET 3 AB 5 THR A 392 HIS A 400 -1 O THR A 392 N PHE A 389
SHEET 4 AB 5 VAL A 441 ASP A 447 1 O VAL A 441 N CYS A 395
SHEET 5 AB 5 ASP A 524 GLY A 530 -1 O ARG A 525 N GLY A 446
SHEET 1 AC 2 GLN A 423 PHE A 424 0
SHEET 2 AC 2 LEU A 434 THR A 435 -1 O LEU A 434 N PHE A 424
LINK OD1 ASN A 275 MG MG A1569 1555 1555 2.40
LINK OE1 GLU A 303 MG MG A1569 1555 1555 2.39
LINK MG MG A1569 O HOH A2018 1555 1555 2.43
LINK MG MG A1569 O HOH A2020 1555 1555 2.46
LINK MG MG A1569 O HOH A2023 1555 1555 2.53
LINK MG MG A1569 O HOH A2050 1555 1555 2.32
CISPEP 1 TYR A 502 LYS A 503 0 0.11
SITE 1 AC1 18 LEU A 306 LYS A 308 PHE A 311 ASN A 379
SITE 2 AC1 18 LYS A 380 ALA A 403 HIS A 404 TYR A 502
SITE 3 AC1 18 LYS A 503 LYS A 516 ARG A 518 HOH A2050
SITE 4 AC1 18 HOH A2051 HOH A2177 HOH A2179 HOH A2314
SITE 5 AC1 18 HOH A2315 HOH A2316
SITE 1 AC2 6 ASN A 275 GLU A 303 HOH A2018 HOH A2020
SITE 2 AC2 6 HOH A2023 HOH A2050
SITE 1 AC3 3 HIS A 541 MET A 542 ALA A 543
SITE 1 AC4 6 SER A 307 LYS A 308 ARG A 376 HOH A2142
SITE 2 AC4 6 HOH A2146 HOH A2317
SITE 1 AC5 10 ILE A 262 GLN A 263 PHE A 265 HIS A 357
SITE 2 AC5 10 TYR A 360 HIS A 390 ASN A 532 ARG A 561
SITE 3 AC5 10 HOH A2123 HOH A2292
CRYST1 133.661 133.661 133.661 90.00 90.00 90.00 P 21 3 12
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 0.007482 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007482 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007482 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
