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 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 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