HEADER CALCIUM BINDING PROTEIN 24-JUL-09 3IF7 TITLE STRUCTURE OF CALMODULIN COMPLEXED WITH ITS FIRST ENDOGENOUS INHIBITOR, TITLE 2 SPHINGOSYLPHOSPHORYLCHOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: BRAIN KEYWDS EF-HAND, PHOSPHOLIPID, CALCIUM BINDING PROTEIN, ISOPEPTIDE BOND, KEYWDS 2 METHYLATION, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.KOVACS,V.HARMAT,J.TOTH,B.G.VERTESSY,K.MODOS,J.KARDOS,K.LILIOM REVDAT 4 01-NOV-23 3IF7 1 REMARK REVDAT 3 13-JUL-11 3IF7 1 VERSN REVDAT 2 13-OCT-10 3IF7 1 JRNL REVDAT 1 30-JUN-10 3IF7 0 JRNL AUTH E.KOVACS,V.HARMAT,J.TOTH,B.G.VERTESSY,K.MODOS,J.KARDOS, JRNL AUTH 2 K.LILIOM JRNL TITL STRUCTURE AND MECHANISM OF CALMODULIN BINDING TO A SIGNALING JRNL TITL 2 SPHINGOLIPID REVEAL NEW ASPECTS OF LIPID-PROTEIN JRNL TITL 3 INTERACTIONS JRNL REF FASEB J. V. 24 3829 2010 JRNL REFN ISSN 0892-6638 JRNL PMID 20522785 JRNL DOI 10.1096/FJ.10-155614 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20426 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1103 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1478 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -0.63000 REMARK 3 B12 (A**2) : 0.21000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.380 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1187 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 809 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1593 ; 2.085 ; 2.022 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1987 ; 1.113 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 146 ; 5.323 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;34.967 ;26.034 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 199 ;14.874 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;21.654 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 177 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1287 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 221 ; 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): 707 ; 1.765 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 295 ; 0.578 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1128 ; 2.965 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 480 ; 3.897 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 462 ; 6.469 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 78 REMARK 3 RESIDUE RANGE : A 149 A 150 REMARK 3 ORIGIN FOR THE GROUP (A): -35.7467 14.8822 -10.9215 REMARK 3 T TENSOR REMARK 3 T11: 0.0205 T22: 0.0444 REMARK 3 T33: 0.0202 T12: 0.0187 REMARK 3 T13: -0.0151 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 2.1851 L22: 0.0378 REMARK 3 L33: 2.8429 L12: 0.1365 REMARK 3 L13: 1.4153 L23: -0.1370 REMARK 3 S TENSOR REMARK 3 S11: 0.1095 S12: -0.0012 S13: -0.1478 REMARK 3 S21: 0.0093 S22: -0.0073 S23: -0.0078 REMARK 3 S31: 0.0872 S32: 0.1803 S33: -0.1021 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 81 A 146 REMARK 3 RESIDUE RANGE : A 151 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): -20.5413 17.7005 -22.1840 REMARK 3 T TENSOR REMARK 3 T11: 0.0057 T22: 0.0126 REMARK 3 T33: 0.0284 T12: -0.0030 REMARK 3 T13: 0.0045 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 2.6177 L22: 1.7183 REMARK 3 L33: 1.4050 L12: -0.2779 REMARK 3 L13: -0.4056 L23: -0.1350 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0657 S13: 0.0688 REMARK 3 S21: 0.0737 S22: 0.0077 S23: 0.1666 REMARK 3 S31: 0.0217 S32: -0.1013 S33: -0.0152 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 153 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): -27.6450 14.4227 -16.0693 REMARK 3 T TENSOR REMARK 3 T11: 0.1954 T22: 0.2613 REMARK 3 T33: 0.2715 T12: 0.0362 REMARK 3 T13: 0.0371 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.3295 L22: 1.1767 REMARK 3 L33: 7.8380 L12: -0.6195 REMARK 3 L13: 1.4920 L23: -2.6996 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: -0.0389 S13: -0.1080 REMARK 3 S21: 0.1122 S22: 0.1188 S23: 0.2436 REMARK 3 S31: 0.0777 S32: -0.0167 S33: -0.0848 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3IF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21596 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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: N- AND C-TERMINAL DOMAINS OF PDB ENTRY 1LIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE, 10MM CACL2, REMARK 280 10MM MGCL2, 28% PEG 8000: MIXED WITH 10MM LIPID IN METHANOL REMARK 280 SOLUTION AND 1MM PROTEIN SOLUTION, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 113.56000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.78000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 56.78000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 113.56000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HOH A 164 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 ALA A 1 REMARK 465 ASP A 2 REMARK 465 THR A 79 REMARK 465 ASP A 80 REMARK 465 ALA A 147 REMARK 465 LYS A 148 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 GLU A 7 CG CD OE1 OE2 REMARK 470 ASN A 42 CG OD1 ND2 REMARK 470 GLU A 47 CD OE1 OE2 REMARK 470 LYS A 75 CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 ASP A 78 CB CG OD1 OD2 REMARK 470 SER A 81 OG REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 LYS A 115 CD CE NZ REMARK 470 ASP A 122 CG OD1 OD2 REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 183 O HOH A 211 6454 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 55 CB VAL A 55 CG2 -0.142 REMARK 500 TYR A 138 CE1 TYR A 138 CZ -0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 75 -148.67 57.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPU A 153 REMARK 610 SPU A 154 REMARK 610 SPU A 155 REMARK 610 SPU A 156 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 CA A 149 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 22 OD1 81.2 REMARK 620 3 ASP A 24 OD1 86.8 80.1 REMARK 620 4 THR A 26 O 82.8 155.6 80.8 REMARK 620 5 GLU A 31 OE1 109.4 127.0 149.3 75.8 REMARK 620 6 GLU A 31 OE2 94.4 75.3 154.9 124.3 52.7 REMARK 620 7 HOH A 160 O 160.2 79.3 86.3 114.2 85.5 84.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 ASP A 58 OD1 81.8 REMARK 620 3 ASN A 60 OD1 88.6 77.9 REMARK 620 4 THR A 62 O 82.9 150.2 76.3 REMARK 620 5 GLU A 67 OE1 100.8 126.4 154.7 81.6 REMARK 620 6 GLU A 67 OE2 87.4 74.7 152.6 129.9 52.2 REMARK 620 7 HOH A 157 O 164.2 83.2 92.9 112.7 84.4 84.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 151 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD1 REMARK 620 2 ASP A 95 OD1 79.9 REMARK 620 3 ASN A 97 OD1 84.8 78.3 REMARK 620 4 TYR A 99 O 86.2 156.7 82.0 REMARK 620 5 GLU A 104 OE1 104.1 126.2 154.7 75.1 REMARK 620 6 GLU A 104 OE2 95.3 74.5 152.3 125.7 51.8 REMARK 620 7 HOH A 180 O 165.4 85.5 91.4 107.4 85.2 81.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 152 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 131 OD1 79.2 REMARK 620 3 ASP A 133 OD1 93.0 77.8 REMARK 620 4 GLN A 135 O 88.8 152.2 77.9 REMARK 620 5 GLU A 140 OE1 107.1 127.0 150.0 80.4 REMARK 620 6 GLU A 140 OE2 82.1 79.2 157.0 124.2 51.2 REMARK 620 7 HOH A 158 O 167.2 88.2 81.6 101.3 82.6 98.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPU A 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPU A 154 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPU A 155 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPU A 156 DBREF 3IF7 A 1 148 UNP P62157 CALM_BOVIN 2 149 SEQRES 1 A 148 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 148 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 148 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 148 GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 148 ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 148 PRO GLU PHE LEU THR MET MET ALA ARG LYS MET LYS ASP SEQRES 7 A 148 THR ASP SER GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL SEQRES 8 A 148 PHE ASP LYS ASP GLY ASN GLY TYR ILE SER ALA ALA GLU SEQRES 9 A 148 LEU ARG HIS VAL MET THR ASN LEU GLY GLU LYS LEU THR SEQRES 10 A 148 ASP GLU GLU VAL ASP GLU MET ILE ARG GLU ALA ASP ILE SEQRES 11 A 148 ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN SEQRES 12 A 148 MET MET THR ALA LYS HET CA A 149 1 HET CA A 150 1 HET CA A 151 1 HET CA A 152 1 HET SPU A 153 28 HET SPU A 154 22 HET SPU A 155 23 HET SPU A 156 7 HETNAM CA CALCIUM ION HETNAM SPU 2-{[(R)-{[(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1- HETNAM 2 SPU YL]OXY}(HYDROXY)PHOSPHORYL]OXY}-N,N,N- HETNAM 3 SPU TRIMETHYLETHANAMINIUM HETSYN SPU SPHINGOSYLPHOSPHORYLCHOLINE, SPHINGOSINE HETSYN 2 SPU PHOSPHORYLCHOLINE FORMUL 2 CA 4(CA 2+) FORMUL 6 SPU 4(C23 H50 N2 O5 P 1+) FORMUL 10 HOH *79(H2 O) HELIX 1 1 THR A 5 ASP A 20 1 16 HELIX 2 2 THR A 28 LEU A 39 1 12 HELIX 3 3 THR A 44 ASP A 56 1 13 HELIX 4 4 PHE A 65 LYS A 75 1 11 HELIX 5 5 SER A 81 ASP A 93 1 13 HELIX 6 6 SER A 101 LEU A 112 1 12 HELIX 7 7 THR A 117 ASP A 129 1 13 HELIX 8 8 TYR A 138 THR A 146 1 9 SHEET 1 A 2 THR A 26 ILE A 27 0 SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE A 27 SHEET 1 B 2 TYR A 99 ILE A 100 0 SHEET 2 B 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE A 100 LINK OD1 ASP A 20 CA CA A 149 1555 1555 2.34 LINK OD1 ASP A 22 CA CA A 149 1555 1555 2.36 LINK OD1 ASP A 24 CA CA A 149 1555 1555 2.40 LINK O THR A 26 CA CA A 149 1555 1555 2.30 LINK OE1 GLU A 31 CA CA A 149 1555 1555 2.45 LINK OE2 GLU A 31 CA CA A 149 1555 1555 2.49 LINK OD1 ASP A 56 CA CA A 150 1555 1555 2.20 LINK OD1 ASP A 58 CA CA A 150 1555 1555 2.40 LINK OD1 ASN A 60 CA CA A 150 1555 1555 2.36 LINK O THR A 62 CA CA A 150 1555 1555 2.24 LINK OE1 GLU A 67 CA CA A 150 1555 1555 2.41 LINK OE2 GLU A 67 CA CA A 150 1555 1555 2.52 LINK OD1 ASP A 93 CA CA A 151 1555 1555 2.31 LINK OD1 ASP A 95 CA CA A 151 1555 1555 2.37 LINK OD1 ASN A 97 CA CA A 151 1555 1555 2.41 LINK O TYR A 99 CA CA A 151 1555 1555 2.24 LINK OE1 GLU A 104 CA CA A 151 1555 1555 2.44 LINK OE2 GLU A 104 CA CA A 151 1555 1555 2.46 LINK OD1 ASP A 129 CA CA A 152 1555 1555 2.35 LINK OD1 ASP A 131 CA CA A 152 1555 1555 2.34 LINK OD1 ASP A 133 CA CA A 152 1555 1555 2.34 LINK O GLN A 135 CA CA A 152 1555 1555 2.34 LINK OE1 GLU A 140 CA CA A 152 1555 1555 2.43 LINK OE2 GLU A 140 CA CA A 152 1555 1555 2.53 LINK CA CA A 149 O HOH A 160 1555 1555 2.43 LINK CA CA A 150 O HOH A 157 1555 1555 2.26 LINK CA CA A 151 O HOH A 180 1555 1555 2.24 LINK CA CA A 152 O HOH A 158 1555 1555 2.34 SITE 1 AC1 6 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 6 GLU A 31 HOH A 160 SITE 1 AC2 6 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 6 GLU A 67 HOH A 157 SITE 1 AC3 6 ASP A 93 ASP A 95 ASN A 97 TYR A 99 SITE 2 AC3 6 GLU A 104 HOH A 180 SITE 1 AC4 6 ASP A 129 ASP A 131 ASP A 133 GLN A 135 SITE 2 AC4 6 GLU A 140 HOH A 158 SITE 1 AC5 12 GLU A 11 MET A 76 ALA A 88 PHE A 92 SITE 2 AC5 12 GLU A 123 MET A 124 GLU A 127 PHE A 141 SITE 3 AC5 12 MET A 144 MET A 145 SPU A 154 SPU A 156 SITE 1 AC6 6 GLU A 11 LEU A 39 GLU A 87 MET A 124 SITE 2 AC6 6 SPU A 153 SPU A 155 SITE 1 AC7 10 PHE A 12 ALA A 15 LEU A 32 MET A 51 SITE 2 AC7 10 GLU A 54 VAL A 55 MET A 71 MET A 72 SITE 3 AC7 10 SPU A 154 SPU A 156 SITE 1 AC8 3 MET A 145 SPU A 153 SPU A 155 CRYST1 39.669 39.669 170.340 90.00 90.00 120.00 P 32 2 1 6 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 0.025209 0.014554 0.000000 0.00000 SCALE2 0.000000 0.029108 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005871 0.00000