HEADER CALCIUM-BINDING PROTEIN 11-MAR-97 6ICB OBSLTE 25-APR-01 6ICB 1IGV TITLE BOVINE CALBINDIN D9K BINDING MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALBINDIN D9K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EF-HAND; COMPND 5 SYNONYM: INTESTINAL CALCIUM BINDING PROTEIN MINOR A FORM; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 STRAIN: MM294; SOURCE 5 CELLULAR_LOCATION: INTRACELLULAR; SOURCE 6 GENE: SYNTHETIC GENE; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MM294; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PICB1; SOURCE 11 EXPRESSION_SYSTEM_GENE: SYNTHETIC GENE KEYWDS CALCIUM-BINDING PROTEIN, EF-HAND, MANGANESE BINDING EXPDTA X-RAY DIFFRACTION AUTHOR E.M.ANDERSSON REVDAT 1 17-SEP-97 6ICB 0 JRNL AUTH M.ANDERSSON,A.MALMENDAL,S.LINSE,I.IVARSSON, JRNL AUTH 2 S.FORSEN,L.A.SVENSSON JRNL TITL STRUCTURAL BASIS FOR THE NEGATIVE ALLOSTERY JRNL TITL 2 BETWEEN CA(2+)-AND MG(2+)-BINDING IN THE JRNL TITL 3 INTRACELLULAR CA(2+)-RECEPTOR CALBINDIN D9K JRNL REF PROTEIN SCI. V. 6 1139 1997 JRNL REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.1 REMARK 3 NUMBER OF REFLECTIONS : 5845 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 SET) : 0.190 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 626 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 509 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 62 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.10 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 10.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.47 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.650 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.130 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : PARAM_MN.ION REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19_MOD.SOL REMARK 3 TOPOLOGY FILE 3 : TOP_MN.ION REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESOLUTION-DEPENDENT WEIGHTING REMARK 4 REMARK 4 6ICB COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 THE SIDE CHAIN ATOMS OF RESIDUE 51 WERE NOT FOUND IN THE REMARK 6 ELECTRON DENSITY. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-1995 REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU/MSC RU-H2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MAR RESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : MARSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 19.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: MG-CALBINDIN D9K REMARK 200 REMARK 200 REMARK: MN-CALBINDIN D9K WERE USED AS A DERIVATIVE FOR MIR REMARK 200 SOLUTION OF MG-CALBINDIN D9K REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,3/4+Z REMARK 290 4555 1/2+Y,1/2-X,1/4+Z REMARK 290 5555 1/2-X,1/2+Y,3/4-Z REMARK 290 6555 1/2+X,1/2-Y,1/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 64.73500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.90000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.10250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.90000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.90000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.36750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.90000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.10250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.90000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.36750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.73500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 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 51 CG CD OE1 OE2 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 1 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: PROGRAM DSSP REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: PROGRAM DSSP REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MSE REMARK 800 SITE_DESCRIPTION: MN BINDING EF-HAND LOOP. REMARK 999 REMARK 999 SEQUENCE REMARK 999 6ICB SWS P02633 1 - 2 NOT IN ATOMS LIST REMARK 999 REMARK 999 MET 0 WAS INTRODUCED DURING EXPRESSION. DBREF 6ICB A 1 75 UNP P02633 S10D_BOVIN 4 78 SEQRES 1 A 76 MET LYS SER PRO GLU GLU LEU LYS GLY ILE PHE GLU LYS SEQRES 2 A 76 TYR ALA ALA LYS GLU GLY ASP PRO ASN GLN LEU SER LYS SEQRES 3 A 76 GLU GLU LEU LYS LEU LEU LEU GLN THR GLU PHE PRO SER SEQRES 4 A 76 LEU LEU LYS GLY PRO SER THR LEU ASP GLU LEU PHE GLU SEQRES 5 A 76 GLU LEU ASP LYS ASN GLY ASP GLY GLU VAL SER PHE GLU SEQRES 6 A 76 GLU PHE GLN VAL LEU VAL LYS LYS ILE SER GLN HET MN 78 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN MN 2+ FORMUL 3 HOH *36(H2 O1) HELIX 1 I SER A 2 ALA A 14 1 13 HELIX 2 II SER A 24 GLU A 35 1 12 HELIX 3 L PHE A 36 LEU A 40 5 5 HELIX 4 III THR A 45 ASP A 54 1 10 HELIX 5 IV SER A 62 ILE A 73 1 12 SHEET 1 S1 2 LEU A 23 LEU A 23 0 SHEET 2 S1 2 VAL A 61 VAL A 61 -1 LINK MN MN 78 OD1 ASP A 54 LINK MN MN 78 OD1 ASN A 56 LINK MN MN 78 OD1 ASP A 58 LINK MN MN 78 O GLU A 60 SITE 1 MSE 4 ASP A 54 ASN A 56 ASP A 58 GLU A 60 CRYST1 33.800 33.800 129.470 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007724 0.00000