HEADER METAL BINDING PROTEIN 23-OCT-00 1G33 TITLE CRYSTAL STRUCTURE OF RAT PARVALBUMIN WITHOUT THE N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARVALBUMIN ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 37-109; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS CALCIUM-BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.THEPAUT,M.P.STRUB,A.CAVE,J.L.BANERES,M.W.BERCHTOLD,C.DUMAS, AUTHOR 2 A.PADILLA REVDAT 3 03-NOV-21 1G33 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1G33 1 VERSN REVDAT 1 03-OCT-01 1G33 0 JRNL AUTH M.THEPAUT,M.P.STRUB,A.CAVE,J.L.BANERES,M.W.BERCHTOLD, JRNL AUTH 2 C.DUMAS,A.PADILLA JRNL TITL STRUCTURE OF RAT PARVALBUMIN WITH DELETED AB DOMAIN: JRNL TITL 2 IMPLICATIONS FOR THE EVOLUTION OF EF HAND CALCIUM-BINDING JRNL TITL 3 PROTEINS AND POSSIBLE PHYSIOLOGICAL RELEVANCE. JRNL REF PROTEINS V. 45 117 2001 JRNL REFN ISSN 0887-3585 JRNL PMID 11562941 JRNL DOI 10.1002/PROT.1131 REMARK 2 REMARK 2 RESOLUTION. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 11866 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) : 0.169 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1224 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1232 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 149 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 550 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 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) : 2.090 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.840 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.700 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.740 ; 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARAM.SO4 REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOP.SO4 REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1G33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 169765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 34.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25900 REMARK 200 FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1RTP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE 3M, CALCIUM CHLORIDE REMARK 280 30MM, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.34000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.34000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 327 LIES ON A SPECIAL POSITION. 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 110 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 ASP A 53 OD1 82.6 REMARK 620 3 SER A 55 OG 88.5 80.0 REMARK 620 4 PHE A 57 O 84.4 150.8 73.6 REMARK 620 5 GLU A 59 OE1 170.3 102.2 84.1 87.5 REMARK 620 6 GLU A 62 OE1 104.5 126.3 151.4 82.3 79.6 REMARK 620 7 GLU A 62 OE2 99.0 74.1 151.8 133.9 90.4 52.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 111 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD1 REMARK 620 2 ASP A 92 OD1 83.4 REMARK 620 3 ASP A 94 OD1 87.3 79.5 REMARK 620 4 LYS A 96 O 83.5 154.2 77.7 REMARK 620 5 GLU A 101 OE1 109.0 126.0 150.1 79.5 REMARK 620 6 GLU A 101 OE2 91.9 75.6 155.1 127.0 52.3 REMARK 620 7 HOH A 312 O 168.6 92.7 81.4 95.8 82.0 97.5 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 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 200 DBREF 1G33 A 37 109 UNP P02625 PRVA_RAT 37 109 SEQADV 1G33 MET A 37 UNP P02625 LYS 37 ENGINEERED MUTATION SEQRES 1 A 73 MET LYS SER ALA ASP ASP VAL LYS LYS VAL PHE HIS ILE SEQRES 2 A 73 LEU ASP LYS ASP LYS SER GLY PHE ILE GLU GLU ASP GLU SEQRES 3 A 73 LEU GLY SER ILE LEU LYS GLY PHE SER SER ASP ALA ARG SEQRES 4 A 73 ASP LEU SER ALA LYS GLU THR LYS THR LEU MET ALA ALA SEQRES 5 A 73 GLY ASP LYS ASP GLY ASP GLY LYS ILE GLY VAL GLU GLU SEQRES 6 A 73 PHE SER THR LEU VAL ALA GLU SER HET CA A 110 1 HET CA A 111 1 HET SO4 A 200 5 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION FORMUL 2 CA 2(CA 2+) FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *47(H2 O) HELIX 1 1 SER A 39 ASP A 51 1 13 HELIX 2 2 GLU A 59 GLY A 64 1 6 HELIX 3 3 SER A 65 SER A 71 1 7 HELIX 4 4 SER A 78 ASP A 90 1 13 HELIX 5 5 GLY A 98 VAL A 106 1 9 LINK OD1 ASP A 51 CA CA A 110 1555 1555 2.32 LINK OD1 ASP A 53 CA CA A 110 1555 1555 2.38 LINK OG SER A 55 CA CA A 110 1555 1555 2.58 LINK O PHE A 57 CA CA A 110 1555 1555 2.38 LINK OE1 GLU A 59 CA CA A 110 1555 1555 2.35 LINK OE1 GLU A 62 CA CA A 110 1555 1555 2.45 LINK OE2 GLU A 62 CA CA A 110 1555 1555 2.49 LINK OD1 ASP A 90 CA CA A 111 1555 1555 2.33 LINK OD1 ASP A 92 CA CA A 111 1555 1555 2.40 LINK OD1 ASP A 94 CA CA A 111 1555 1555 2.43 LINK O LYS A 96 CA CA A 111 1555 1555 2.40 LINK OE1 GLU A 101 CA CA A 111 1555 1555 2.47 LINK OE2 GLU A 101 CA CA A 111 1555 1555 2.58 LINK CA CA A 111 O HOH A 312 1555 1555 2.44 SITE 1 AC1 6 ASP A 51 ASP A 53 SER A 55 PHE A 57 SITE 2 AC1 6 GLU A 59 GLU A 62 SITE 1 AC2 6 ASP A 90 ASP A 92 ASP A 94 LYS A 96 SITE 2 AC2 6 GLU A 101 HOH A 312 SITE 1 AC3 8 GLY A 98 VAL A 99 GLU A 100 GLU A 101 SITE 2 AC3 8 HOH A 312 HOH A 325 HOH A 327 HOH A 339 CRYST1 48.930 50.680 25.610 90.00 90.00 90.00 P 21 21 2 4 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 0.020437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039047 0.00000