HEADER METAL BINDING PROTEIN 20-NOV-98 1B1G TITLE SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CALBINDIN D9K); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INTESTINAL CALCIUM-BINDING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3) KEYWDS CALCIUM-BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.KORDEL,D.A.PEARLMAN,W.J.CHAZIN REVDAT 6 27-DEC-23 1B1G 1 REMARK LINK REVDAT 5 10-AUG-11 1B1G 1 REMARK REVDAT 4 24-FEB-09 1B1G 1 VERSN REVDAT 3 22-DEC-99 1B1G 4 HEADER COMPND REMARK JRNL REVDAT 3 2 4 ATOM SOURCE SEQRES REVDAT 2 02-DEC-98 1B1G 1 REMARK SEQRES REVDAT 1 25-NOV-98 1B1G 0 JRNL AUTH J.KORDEL,D.A.PEARLMAN,W.J.CHAZIN JRNL TITL PROTEIN SOLUTION STRUCTURE CALCULATIONS IN SOLUTION: JRNL TITL 2 SOLVATED MOLECULAR DYNAMICS REFINEMENT OF CALBINDIN D9K. JRNL REF J.BIOMOL.NMR V. 10 231 1997 JRNL REFN ISSN 0925-2738 JRNL PMID 9390401 JRNL DOI 10.1023/A:1018383102870 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.KORDEL,N.J.SKELTON,M.AKKE,W.J.CHAZIN REMARK 1 TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF CALCIUM-LOADED REMARK 1 TITL 2 CALBINDIN D9K REMARK 1 REF J.MOL.BIOL. V. 231 711 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.KORDEL,S.FORSEN,T.DRAKENBERG,W.J.CHAZIN REMARK 1 TITL THE RATE AND STRUCTURAL CONSEQUENCES OF PROLINE CIS-TRANS REMARK 1 TITL 2 ISOMERIZATION IN CALBINDIN D9K: NMR STUDIES OF THE MINOR REMARK 1 TITL 3 (CIS-PRO43) ISOFORM AND THE PRO43GLY MUTANT REMARK 1 REF BIOCHEMISTRY V. 29 4400 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.KORDEL,S.FORSEN,W.J.CHAZIN REMARK 1 TITL 1H NMR SEQUENTIAL RESONANCE ASSIGNMENTS, SECONDARY REMARK 1 TITL 2 STRUCTURE, AND GLOBAL FOLD IN SOLUTION OF THE MAJOR REMARK 1 TITL 3 (TRANS-PRO43) FORM OF BOVINE CALBINDIN D9K REMARK 1 REF BIOCHEMISTRY V. 28 7065 1989 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.M.E.SZEBENYI,K.MOFFAT REMARK 1 TITL THE REFINED STRUCTURE OF VITAMIN D-DEPENDENT CALCIUM-BINDING REMARK 1 TITL 2 PROTEIN FROM BOVINE INTESTINE. MOLECULAR DETAILS, ION REMARK 1 TITL 3 BINDING, AND IMPLICATIONS FOR THE STRUCTURE OF OTHER REMARK 1 TITL 4 CALCIUM-BINDING PROTEINS REMARK 1 REF J.BIOL.CHEM. V. 261 8761 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.0 REMARK 3 AUTHORS : REMARK 3 D.A.PEARLMAN,D.A.CASE,J.C.CALDWELL,G.L.SEIBEL,U.C.SINGH,P.WEINER REMARK 3 AND P.A.KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PREVIOUSLY CALCULATED DISGEO STRUCTURES WERE PLACED IN A BATH OF REMARK 3 WATER REMARK 3 MOLECULES AND CALCIUM IONS WERE ADDED IN THE BINDING SITES. THE REMARK 3 SYSTEM WAS REMARK 3 ENERGY MINIMIZED TO REMOVE BAD CONTACTS, THEN ANNEALED AT 300 K. REMARK 3 DETAILS CAN REMARK 3 BE FOUND IN THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1B1G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000118. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISGEO, AMBER REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED REMARK 210 MD WITH EXPLICIT SOLVENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CONFORMERS USED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: AUTHOR USED THE NMR DATA FROM ENTRY 2BCB. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 4 PHE A 36 CB - CG - CD1 ANGL. DEV. = -4.7 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 1 GLU A 17 -146.98 -88.81 REMARK 500 1 SER A 44 125.67 -35.85 REMARK 500 1 ASN A 56 52.94 -174.49 REMARK 500 1 ASP A 58 -30.09 100.22 REMARK 500 2 ASP A 19 142.63 64.54 REMARK 500 2 LEU A 40 7.81 -67.52 REMARK 500 2 ASN A 56 -42.01 -134.76 REMARK 500 2 ASP A 58 65.05 162.09 REMARK 500 3 LYS A 41 -82.08 -72.02 REMARK 500 3 LYS A 55 0.05 -67.05 REMARK 500 3 ASN A 56 -50.99 -153.15 REMARK 500 3 ASP A 58 6.92 -163.19 REMARK 500 3 GLU A 60 -161.44 -74.07 REMARK 500 4 GLU A 17 -104.70 -84.30 REMARK 500 4 ASP A 19 136.60 57.88 REMARK 500 4 SER A 44 95.86 57.17 REMARK 500 5 ASP A 19 101.28 66.35 REMARK 500 5 SER A 44 -52.07 -147.34 REMARK 500 5 LEU A 53 -70.04 -59.82 REMARK 500 5 ASN A 56 -23.87 -153.08 REMARK 500 5 ASP A 58 20.68 -166.17 REMARK 500 5 GLU A 60 -156.11 -83.15 REMARK 500 6 LEU A 40 63.37 -69.75 REMARK 500 6 THR A 45 -177.10 -65.76 REMARK 500 6 ASN A 56 67.10 -151.91 REMARK 500 6 ASP A 58 15.24 121.29 REMARK 500 7 LYS A 41 49.24 -78.32 REMARK 500 7 ASN A 56 -45.53 -142.37 REMARK 500 7 ASP A 58 -6.11 -166.64 REMARK 500 7 GLU A 60 -162.92 -77.72 REMARK 500 8 LEU A 40 32.02 -73.91 REMARK 500 8 SER A 44 -162.78 62.52 REMARK 500 8 ASP A 58 44.52 141.36 REMARK 500 8 GLU A 60 -163.97 -79.50 REMARK 500 8 SER A 74 42.84 -92.38 REMARK 500 9 ASP A 19 133.53 60.33 REMARK 500 9 THR A 34 -68.43 -96.87 REMARK 500 9 LEU A 40 28.03 -73.90 REMARK 500 9 LYS A 41 70.30 36.74 REMARK 500 9 ASP A 58 -36.07 -135.75 REMARK 500 10 ASN A 56 -31.23 -151.15 REMARK 500 10 ASP A 58 18.68 -177.12 REMARK 500 10 GLU A 60 -157.85 -80.85 REMARK 500 10 GLU A 64 -62.95 -27.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 57 ASP A 58 1 61.88 REMARK 500 ASP A 58 GLY A 59 2 -140.74 REMARK 500 GLY A 57 ASP A 58 3 -138.83 REMARK 500 ASP A 58 GLY A 59 3 -134.72 REMARK 500 ASP A 58 GLY A 59 5 -128.26 REMARK 500 GLY A 57 ASP A 58 7 -137.61 REMARK 500 ASP A 58 GLY A 59 7 -131.68 REMARK 500 GLY A 59 GLU A 60 7 -147.17 REMARK 500 GLY A 59 GLU A 60 8 -145.18 REMARK 500 GLY A 42 GLY A 43 10 -149.04 REMARK 500 ASP A 58 GLY A 59 10 -141.68 REMARK 500 GLY A 59 GLU A 60 10 -144.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 10 0.13 SIDE CHAIN REMARK 500 2 PHE A 10 0.20 SIDE CHAIN REMARK 500 2 PHE A 36 0.08 SIDE CHAIN REMARK 500 2 PHE A 50 0.11 SIDE CHAIN REMARK 500 3 PHE A 10 0.17 SIDE CHAIN REMARK 500 3 TYR A 13 0.13 SIDE CHAIN REMARK 500 3 PHE A 36 0.08 SIDE CHAIN REMARK 500 3 PHE A 50 0.09 SIDE CHAIN REMARK 500 4 PHE A 10 0.17 SIDE CHAIN REMARK 500 4 TYR A 13 0.10 SIDE CHAIN REMARK 500 4 PHE A 36 0.14 SIDE CHAIN REMARK 500 5 PHE A 10 0.19 SIDE CHAIN REMARK 500 5 PHE A 36 0.08 SIDE CHAIN REMARK 500 5 PHE A 50 0.09 SIDE CHAIN REMARK 500 6 PHE A 10 0.17 SIDE CHAIN REMARK 500 7 PHE A 10 0.17 SIDE CHAIN REMARK 500 7 PHE A 50 0.10 SIDE CHAIN REMARK 500 8 PHE A 10 0.16 SIDE CHAIN REMARK 500 8 PHE A 50 0.09 SIDE CHAIN REMARK 500 9 PHE A 10 0.16 SIDE CHAIN REMARK 500 10 PHE A 10 0.18 SIDE CHAIN REMARK 500 10 TYR A 13 0.11 SIDE CHAIN REMARK 500 10 PHE A 36 0.13 SIDE CHAIN REMARK 500 10 PHE A 50 0.09 SIDE CHAIN 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 76 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 14 O REMARK 620 2 GLU A 17 OE2 130.3 REMARK 620 3 ASP A 19 O 70.1 75.4 REMARK 620 4 ASP A 19 OD2 92.2 106.6 67.7 REMARK 620 5 GLN A 22 O 71.5 157.7 122.6 73.0 REMARK 620 6 GLU A 27 OE2 71.7 81.9 101.7 163.4 104.7 REMARK 620 7 GLU A 27 OE1 103.0 94.0 155.6 136.6 73.9 54.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 77 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 54 OD2 REMARK 620 2 ASP A 54 OD1 43.0 REMARK 620 3 GLY A 57 O 72.2 64.9 REMARK 620 4 GLU A 60 O 75.1 117.1 90.7 REMARK 620 5 GLU A 65 OE2 81.4 73.0 137.5 114.3 REMARK 620 N 1 2 3 4 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 76 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 77 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BCB RELATED DB: PDB DBREF 1B1G A 1 75 UNP P02633 S100G_BOVIN 4 78 SEQRES 1 A 75 LYS SER PRO GLU GLU LEU LYS GLY ILE PHE GLU LYS TYR SEQRES 2 A 75 ALA ALA LYS GLU GLY ASP PRO ASN GLN LEU SER LYS GLU SEQRES 3 A 75 GLU LEU LYS LEU LEU LEU GLN THR GLU PHE PRO SER LEU SEQRES 4 A 75 LEU LYS GLY GLY SER THR LEU ASP GLU LEU PHE GLU GLU SEQRES 5 A 75 LEU ASP LYS ASN GLY ASP GLY GLU VAL SER PHE GLU GLU SEQRES 6 A 75 PHE GLN VAL LEU VAL LYS LYS ILE SER GLN HET CA A 76 1 HET CA A 77 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 PRO A 3 ALA A 15 1 13 HELIX 2 2 LYS A 25 GLU A 35 1 11 HELIX 3 3 LEU A 46 LEU A 53 1 8 HELIX 4 4 PHE A 63 LYS A 72 1 10 SHEET 1 A 2 LEU A 23 SER A 24 0 SHEET 2 A 2 GLU A 60 VAL A 61 -1 N VAL A 61 O LEU A 23 LINK O ALA A 14 CA CA A 76 1555 1555 2.35 LINK OE2 GLU A 17 CA CA A 76 1555 1555 2.27 LINK O ASP A 19 CA CA A 76 1555 1555 2.69 LINK OD2 ASP A 19 CA CA A 76 1555 1555 2.26 LINK O GLN A 22 CA CA A 76 1555 1555 2.38 LINK OE2 GLU A 27 CA CA A 76 1555 1555 2.35 LINK OE1 GLU A 27 CA CA A 76 1555 1555 2.38 LINK OD2 ASP A 54 CA CA A 77 1555 1555 2.25 LINK OD1 ASP A 54 CA CA A 77 1555 1555 3.22 LINK O GLY A 57 CA CA A 77 1555 1555 2.36 LINK O GLU A 60 CA CA A 77 1555 1555 2.36 LINK OE2 GLU A 65 CA CA A 77 1555 1555 2.28 CISPEP 1 GLY A 43 SER A 44 5 7.27 SITE 1 AC1 5 ALA A 14 GLU A 17 ASP A 19 GLN A 22 SITE 2 AC1 5 GLU A 27 SITE 1 AC2 4 ASP A 54 GLY A 57 GLU A 60 GLU A 65 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1