PDB Short entry for 1BU3 HEADER CALCIUM BINDING 30-AUG-98 1BU3 TITLE REFINED CRYSTAL STRUCTURE OF CALCIUM-BOUND SILVER HAKE (PI 4.2) TITLE 2 PARVALBUMIN AT 1.65 A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CALCIUM-BINDING DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MERLUCCIUS BILINEARIS; SOURCE 3 ORGANISM_COMMON: SILVER HAKE; SOURCE 4 ORGANISM_TAXID: 79698; SOURCE 5 TISSUE: MUSCLE KEYWDS CALCIUM BINDING EXPDTA X-RAY DIFFRACTION AUTHOR R.C.RICHARDSON,D.J.NELSON,W.E.ROYER,D.J.HARRINGTON REVDAT 3 09-AUG-23 1BU3 1 REMARK LINK REVDAT 2 24-FEB-09 1BU3 1 VERSN REVDAT 1 10-AUG-99 1BU3 0 JRNL AUTH R.C.RICHARDSON,N.M.KING,D.J.HARRINGTON,H.SUN,W.E.ROYER, JRNL AUTH 2 D.J.NELSON JRNL TITL X-RAY CRYSTAL STRUCTURE AND MOLECULAR DYNAMICS SIMULATIONS JRNL TITL 2 OF SILVER HAKE PARVALBUMIN (ISOFORM B). JRNL REF PROTEIN SCI. V. 9 73 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 10739249 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.Y.ZHANG,H.SPENO,C.CLAIRMONT,D.J.NELSON REMARK 1 TITL ISOLATION OF AN UNUSUAL PARVALBUMIN FROM THE WHITE MUSCLE OF REMARK 1 TITL 2 THE SILVER HAKE (MERLUCCIUS BILINEARIS) REMARK 1 REF J.INORG.BIOCHEM. V. 40 59 1990 REMARK 1 REFN ISSN 0162-0134 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15685 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) : 0.214 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 803 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.50 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.729 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.440 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BU3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS 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 : 15685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 <I/SIGMA(I)> 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 3.8 REMARK 200 STARTING MODEL: 5CPV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 21.08000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.08000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 37.85500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.36500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.85500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.36500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.08000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.85500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.36500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.08000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.85500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.36500 REMARK 290 SMTRY3 8 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: DIMERIC 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 21.08000 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 107 67.12 63.10 REMARK 500 REMARK 500 REMARK: NULL 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 109 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 51 OD1 REMARK 620 2 ASP A 53 OD1 82.7 REMARK 620 3 SER A 55 OG 91.2 84.3 REMARK 620 4 PHE A 57 O 83.9 157.6 78.2 REMARK 620 5 GLU A 59 OE1 167.8 106.6 82.1 84.8 REMARK 620 6 GLU A 62 OE2 103.2 121.1 151.8 79.4 78.9 REMARK 620 7 GLU A 62 OE1 97.7 71.8 153.0 128.0 92.7 49.4 REMARK 620 N 1 2 3 4 5 6 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 90 OD2 REMARK 620 2 ASP A 92 OD1 82.5 REMARK 620 3 ASP A 94 OD1 81.9 77.9 REMARK 620 4 ALA A 96 O 82.9 150.3 74.4 REMARK 620 5 GLU A 101 OE2 93.0 78.6 156.5 127.9 REMARK 620 6 GLU A 101 OE1 110.6 126.5 152.7 83.0 50.1 REMARK 620 7 HOH A 130 O 163.1 96.3 81.4 90.3 103.3 83.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CD REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CA BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: EF REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CA BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 110 DBREF 1BU3 A 1 108 UNP P56503 PRVB_MERBI 1 108 SEQRES 1 A 109 ACE ALA PHE SER GLY ILE LEU ALA ASP ALA ASP VAL ALA SEQRES 2 A 109 ALA ALA LEU LYS ALA CYS GLU ALA ALA ASP SER PHE ASN SEQRES 3 A 109 TYR LYS ALA PHE PHE ALA LYS VAL GLY LEU THR ALA LYS SEQRES 4 A 109 SER ALA ASP ASP ILE LYS LYS ALA PHE PHE VAL ILE ASP SEQRES 5 A 109 GLN ASP LYS SER GLY PHE ILE GLU GLU ASP GLU LEU LYS SEQRES 6 A 109 LEU PHE LEU GLN VAL PHE SER ALA GLY ALA ARG ALA LEU SEQRES 7 A 109 THR ASP ALA GLU THR LYS ALA PHE LEU LYS ALA GLY ASP SEQRES 8 A 109 SER ASP GLY ASP GLY ALA ILE GLY VAL ASP GLU TRP ALA SEQRES 9 A 109 ALA LEU VAL LYS ALA HET ACE A 0 3 HET CA A 109 1 HET CA A 110 1 HETNAM ACE ACETYL GROUP HETNAM CA CALCIUM ION FORMUL 1 ACE C2 H4 O FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *114(H2 O) HELIX 1 1 ASP A 8 CYS A 18 1 11 HELIX 2 2 TYR A 26 VAL A 33 1 8 HELIX 3 3 LEU A 35 ALA A 37 5 3 HELIX 4 4 ALA A 40 ILE A 50 1 11 HELIX 5 5 GLU A 60 LYS A 64 1 5 HELIX 6 6 PHE A 66 PHE A 70 1 5 HELIX 7 7 ASP A 79 GLY A 89 1 11 HELIX 8 8 VAL A 99 VAL A 106 1 8 SHEET 1 A 2 ILE A 58 GLU A 59 0 SHEET 2 A 2 ALA A 96 ILE A 97 -1 N ILE A 97 O ILE A 58 LINK C ACE A 0 N ALA A 1 1555 1555 1.33 LINK OD1 ASP A 51 CA CA A 109 1555 1555 2.38 LINK OD1 ASP A 53 CA CA A 109 1555 1555 2.30 LINK OG SER A 55 CA CA A 109 1555 1555 2.44 LINK O PHE A 57 CA CA A 109 1555 1555 2.33 LINK OE1 GLU A 59 CA CA A 109 1555 1555 2.43 LINK OE2 GLU A 62 CA CA A 109 1555 1555 2.65 LINK OE1 GLU A 62 CA CA A 109 1555 1555 2.60 LINK OD2 ASP A 90 CA CA A 110 1555 1555 2.46 LINK OD1 ASP A 92 CA CA A 110 1555 1555 2.52 LINK OD1 ASP A 94 CA CA A 110 1555 1555 2.47 LINK O ALA A 96 CA CA A 110 1555 1555 2.31 LINK OE2 GLU A 101 CA CA A 110 1555 1555 2.69 LINK OE1 GLU A 101 CA CA A 110 1555 1555 2.48 LINK CA CA A 110 O HOH A 130 1555 1555 2.25 SITE 1 CD 12 ASP A 51 GLN A 52 ASP A 53 LYS A 54 SITE 2 CD 12 SER A 55 GLY A 56 PHE A 57 ILE A 58 SITE 3 CD 12 GLU A 59 GLU A 60 ASP A 61 GLU A 62 SITE 1 EF 12 ASP A 90 SER A 91 ASP A 92 GLY A 93 SITE 2 EF 12 ASP A 94 GLY A 95 ALA A 96 ILE A 97 SITE 3 EF 12 GLY A 98 VAL A 99 ASP A 100 GLU A 101 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 ALA A 96 SITE 2 AC2 6 GLU A 101 HOH A 130 CRYST1 75.710 80.730 42.160 90.00 90.00 90.00 C 2 2 21 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 0.013208 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023719 0.00000 HETATM 1 C ACE A 0 -3.299 20.677 14.578 1.00 28.60 C HETATM 2 O ACE A 0 -4.471 20.880 14.267 1.00 28.60 O HETATM 3 CH3 ACE A 0 -2.821 20.940 15.998 1.00 28.91 C