10 20 30 40 50 60 70 80 1S3P - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER CALCIUM-BINDING PROTEIN 13-JAN-04 1S3P
TITLE CRYSTAL STRUCTURE OF RAT ALPHA-PARVALBUMIN S55D/E59D MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARVALBUMIN ALPHA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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 GENE: PVALB, PVA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT
KEYWDS PARVALBUMIN, EF-HAND, CALCIUM-BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.J.TANNER,M.T.HENZL
REVDAT 2 24-FEB-09 1S3P 1 VERSN REVDAT 1 07-SEP-04 1S3P 0
JRNL AUTH Y.H.LEE,J.J.TANNER,J.D.LARSON,M.T.HENZL JRNL TITL CRYSTAL STRUCTURE OF A HIGH-AFFINITY VARIANT OF JRNL TITL 2 RAT ALPHA-PARVALBUMIN. JRNL REF BIOCHEMISTRY V. 43 10008 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15287728 JRNL DOI 10.1021/BI0492915
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 912248.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 6942 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) : 0.181 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 681 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 623 REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 829 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.50000 REMARK 3 B22 (A**2) : 3.46000 REMARK 3 B33 (A**2) : -0.96000 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.08 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.89 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) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.910 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 38.44 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1S3P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-04. REMARK 100 THE RCSB ID CODE IS RCSB021327.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL REMARK 200 OPTICS : OSMIC CONFOCAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 26.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : 0.14000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.000 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: 1RTP REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION
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 30.73500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.73500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.78500 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER. THERE IS ONE MONOMER REMARK 300 IN THE ASYMMETRIC UNIT.
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 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 210 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 ASP A 53 OD2 85.4 REMARK 620 3 ASP A 55 OD2 87.1 79.4 REMARK 620 4 PHE A 57 O 85.1 155.7 77.8 REMARK 620 5 GLU A 62 OE1 98.1 128.1 152.2 75.5 REMARK 620 6 GLU A 62 OE2 100.2 75.3 152.9 128.5 53.0 REMARK 620 7 HOH A 303 O 173.5 96.8 87.3 90.6 85.5 86.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 211 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD1 REMARK 620 2 ASP A 92 OD1 91.4 REMARK 620 3 ASP A 94 OD1 79.8 84.4 REMARK 620 4 LYS A 96 O 83.3 168.8 85.0 REMARK 620 5 GLU A 101 OE1 129.8 102.4 148.6 88.6 REMARK 620 6 GLU A 101 OE2 86.9 76.6 156.5 112.8 51.4 REMARK 620 7 HOH A 304 O 160.6 94.8 82.5 87.2 66.5 112.4 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 210 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 211 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RWY RELATED DB: PDB
DBREF 1S3P A 1 109 UNP P02625 PRVA_RAT 1 109
SEQADV 1S3P ASP A 55 UNP P02625 SER 55 ENGINEERED SEQADV 1S3P ASP A 59 UNP P02625 GLU 59 ENGINEERED
SEQRES 1 A 109 SER MET THR ASP LEU LEU SER ALA GLU ASP ILE LYS LYS SEQRES 2 A 109 ALA ILE GLY ALA PHE THR ALA ALA ASP SER PHE ASP HIS SEQRES 3 A 109 LYS LYS PHE PHE GLN MET VAL GLY LEU LYS LYS LYS SER SEQRES 4 A 109 ALA ASP ASP VAL LYS LYS VAL PHE HIS ILE LEU ASP LYS SEQRES 5 A 109 ASP LYS ASP GLY PHE ILE ASP GLU ASP GLU LEU GLY SER SEQRES 6 A 109 ILE LEU LYS GLY PHE SER SER ASP ALA ARG ASP LEU SER SEQRES 7 A 109 ALA LYS GLU THR LYS THR LEU MET ALA ALA GLY ASP LYS SEQRES 8 A 109 ASP GLY ASP GLY LYS ILE GLY VAL GLU GLU PHE SER THR SEQRES 9 A 109 LEU VAL ALA GLU SER
HET CA A 210 1 HET CA A 211 1 HET SO4 A 302 5
HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION
FORMUL 2 CA 2(CA 2+) FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *129(H2 O)
HELIX 1 1 SER A 1 LEU A 5 5 5 HELIX 2 2 SER A 7 ALA A 17 1 11 HELIX 3 3 ASP A 25 VAL A 33 1 9 HELIX 4 4 GLY A 34 LYS A 38 5 5 HELIX 5 5 SER A 39 ASP A 51 1 13 HELIX 6 6 ASP A 59 SER A 65 1 7 HELIX 7 7 SER A 65 SER A 71 1 7 HELIX 8 8 SER A 78 ASP A 90 1 13 HELIX 9 9 VAL A 99 GLU A 108 1 10
SHEET 1 A 2 PHE A 57 ILE A 58 0 SHEET 2 A 2 ILE A 97 GLY A 98 -1 O ILE A 97 N ILE A 58
LINK OD1 ASP A 51 CA CA A 210 1555 1555 2.31 LINK OD2 ASP A 53 CA CA A 210 1555 1555 2.40 LINK OD2 ASP A 55 CA CA A 210 1555 1555 2.54 LINK O PHE A 57 CA CA A 210 1555 1555 2.29 LINK OE1 GLU A 62 CA CA A 210 1555 1555 2.35 LINK OE2 GLU A 62 CA CA A 210 1555 1555 2.54 LINK O HOH A 303 CA CA A 210 1555 1555 2.47 LINK OD1 ASP A 90 CA CA A 211 1555 1555 2.30 LINK OD1 ASP A 92 CA CA A 211 1555 1555 2.34 LINK OD1 ASP A 94 CA CA A 211 1555 1555 2.37 LINK O LYS A 96 CA CA A 211 1555 1555 2.29 LINK OE1 GLU A 101 CA CA A 211 1555 1555 2.53 LINK OE2 GLU A 101 CA CA A 211 1555 1555 2.53 LINK O HOH A 304 CA CA A 211 1555 1555 2.50
SITE 1 AC1 6 ASP A 51 ASP A 53 ASP A 55 PHE A 57 SITE 2 AC1 6 GLU A 62 HOH A 303 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 304 SITE 1 AC3 5 LYS A 45 HIS A 48 HOH A 331 HOH A 422 SITE 2 AC3 5 HOH A 428
CRYST1 61.470 51.570 30.750 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 0.016268 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019391 0.000000 0.00000
SCALE3 0.000000 0.000000 0.032520 0.00000