PDB Short entry for 2K2V HEADER CALCIUM-BINDING PROTEIN 13-APR-08 2K2V TITLE ANABAENA CCBP IN THE CALCIUM-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALR1010 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CCBP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANABAENA SP. (STRAIN PCC 7120); SOURCE 3 STRAIN: PCC 7120; SOURCE 4 GENE: CCBP, ALR1010; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS CALCIUM-BINDING, CALCIUM-BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.HU,X.ZHANG,C.JIN REVDAT 2 16-MAR-22 2K2V 1 REMARK LINK REVDAT 1 21-APR-09 2K2V 0 JRNL AUTH Y.HU,X.ZHANG,B.XIA,C.JIN JRNL TITL ANABAENA CCBP IN THE CALCIUM-BOUND FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000100606. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.32 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 40 MM CALCIUM ION, 20 REMARK 210 MM TRIS, 220 MM SODIUM CHLORIDE, REMARK 210 10 MM DTT, 90% H2O/10% D2O; 1 MM REMARK 210 [U-100% 15N] PROTEIN, 40 MM REMARK 210 CALCIUM ION, 20 MM TRIS, 220 MM REMARK 210 SODIUM CHLORIDE, 10 MM DTT, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 2D 1H-13C HSQC; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5, TALOS, REMARK 210 CYANA 2.0, SANE, MOLMOL 2K.2, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 5 ASP A 37 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 ASP A 37 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 8 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 10 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 11 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 12 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 13 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 14 ASP A 37 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 15 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 16 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 17 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 18 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 19 ASP A 37 CB - CG - OD1 ANGL. DEV. = 6.1 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 -54.57 -146.82 REMARK 500 1 GLU A 23 -19.65 -156.25 REMARK 500 1 SER A 56 10.90 -64.92 REMARK 500 1 ASP A 89 21.03 49.85 REMARK 500 1 ASP A 90 12.31 -155.33 REMARK 500 1 TYR A 124 170.84 59.40 REMARK 500 2 GLU A 23 -31.50 -144.91 REMARK 500 2 THR A 55 -98.85 53.85 REMARK 500 2 SER A 56 30.52 -146.02 REMARK 500 2 ASP A 89 10.67 -142.03 REMARK 500 2 ASP A 90 24.33 -150.41 REMARK 500 2 TYR A 124 -152.98 41.80 REMARK 500 2 LYS A 125 -57.59 -128.78 REMARK 500 3 SER A 3 25.82 -140.56 REMARK 500 3 GLU A 17 -53.35 -140.96 REMARK 500 3 GLU A 23 -28.88 -143.08 REMARK 500 3 LYS A 54 -132.79 45.65 REMARK 500 3 SER A 56 15.33 -162.96 REMARK 500 3 CYS A 74 44.23 -78.82 REMARK 500 3 LYS A 88 35.02 -83.24 REMARK 500 3 LYS A 125 10.13 -142.00 REMARK 500 4 VAL A 4 21.98 -145.28 REMARK 500 4 GLU A 23 -20.81 -160.18 REMARK 500 4 ASP A 89 25.66 48.62 REMARK 500 4 ASP A 90 12.38 -153.62 REMARK 500 4 TYR A 124 170.65 -57.94 REMARK 500 5 GLU A 23 -20.02 -154.06 REMARK 500 5 LYS A 88 36.22 -83.79 REMARK 500 5 SER A 98 1.16 -66.41 REMARK 500 6 SER A 3 29.79 -74.69 REMARK 500 6 GLU A 5 -103.99 29.29 REMARK 500 6 ASP A 7 -120.29 37.68 REMARK 500 6 GLU A 23 -27.64 -159.08 REMARK 500 6 CYS A 74 0.22 -69.38 REMARK 500 6 LYS A 88 36.53 -83.03 REMARK 500 7 ASP A 7 48.64 141.40 REMARK 500 7 GLU A 8 4.48 59.94 REMARK 500 7 GLU A 23 -32.81 -160.61 REMARK 500 7 GLU A 41 67.40 -119.00 REMARK 500 7 SER A 52 -162.27 51.53 REMARK 500 7 LYS A 88 -62.21 61.12 REMARK 500 7 ASP A 90 13.37 -152.99 REMARK 500 7 TYR A 124 169.15 57.57 REMARK 500 8 GLU A 23 -18.86 -153.64 REMARK 500 8 THR A 55 162.02 66.37 REMARK 500 8 LYS A 88 -34.38 -145.42 REMARK 500 8 TYR A 124 168.98 59.09 REMARK 500 9 SER A 3 34.42 -144.27 REMARK 500 9 ASP A 7 44.95 -156.57 REMARK 500 9 GLU A 8 16.63 56.70 REMARK 500 REMARK 500 THIS ENTRY HAS 128 RAMACHANDRAN OUTLIERS. 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 ARG A 122 0.08 SIDE CHAIN REMARK 500 8 ARG A 6 0.16 SIDE CHAIN REMARK 500 9 TYR A 93 0.07 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 128 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 O REMARK 620 2 GLU A 23 OE2 111.7 REMARK 620 3 ASP A 24 OD2 133.6 67.2 REMARK 620 4 GLU A 27 OE1 72.5 95.8 61.9 REMARK 620 5 GLU A 27 OE2 82.1 135.4 73.0 46.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 127 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 37 O REMARK 620 2 ASP A 37 OD1 56.4 REMARK 620 3 ASP A 38 O 68.1 112.3 REMARK 620 4 ASP A 38 OD1 99.8 93.0 60.3 REMARK 620 5 LEU A 40 O 58.2 101.3 76.4 136.6 REMARK 620 6 GLU A 41 OE2 119.2 159.7 79.9 107.2 64.8 REMARK 620 N 1 2 3 4 5 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 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 128 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15402 RELATED DB: BMRB REMARK 900 ENTRY CONTAINING CHEMICAL SHIFT ASSIGNMENTS REMARK 900 RELATED ID: 2P0P RELATED DB: PDB REMARK 900 ENTRY CONTAINING THE COORDINATES OF THE CALCIUM-FREE FORM OF THIS REMARK 900 PROTEIN DBREF 2K2V A 1 126 UNP Q8YY42 Q8YY42_ANASP 1 126 SEQRES 1 A 126 MET ALA SER VAL GLU ARG ASP GLU THR ARG GLU HIS ARG SEQRES 2 A 126 ILE GLU THR GLU ILE ILE VAL ASP ALA GLU ASP LYS GLU SEQRES 3 A 126 GLU ARG ALA MET GLY TRP TYR TYR TYR LEU ASP ASP THR SEQRES 4 A 126 LEU GLU PHE PRO PHE MET GLY LYS TRP LYS LYS LYS SER SEQRES 5 A 126 ARG LYS THR SER THR ILE GLU GLU LYS THR VAL GLU VAL SEQRES 6 A 126 LEU GLY MET ALA PRO ASP ASP GLU CYS LEU LYS ASP MET SEQRES 7 A 126 TYR VAL GLU VAL ALA ASP ILE GLY GLY LYS ASP ASP ASP SEQRES 8 A 126 VAL TYR THR ALA LYS LEU SER ASP ILE GLU ALA ILE ASP SEQRES 9 A 126 VAL ASP ASP ASP THR GLN GLU ALA ILE ALA ASP TRP LEU SEQRES 10 A 126 TYR TRP LEU ALA ARG GLY TYR LYS PHE HET CA A 127 1 HET CA A 128 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 GLU A 8 THR A 16 1 9 HELIX 2 2 ASP A 24 LEU A 40 1 17 HELIX 3 3 PRO A 70 LEU A 75 1 6 HELIX 4 4 ASP A 106 GLY A 123 1 18 SHEET 1 A 5 TYR A 93 LYS A 96 0 SHEET 2 A 5 TYR A 79 ASP A 84 -1 N VAL A 82 O TYR A 93 SHEET 3 A 5 ILE A 58 MET A 68 -1 N GLU A 64 O ALA A 83 SHEET 4 A 5 PHE A 44 LYS A 51 -1 N PHE A 44 O VAL A 65 SHEET 5 A 5 ILE A 100 ILE A 103 -1 O ILE A 103 N MET A 45 LINK O ASP A 21 CA CA A 128 1555 1555 2.91 LINK OE2 GLU A 23 CA CA A 128 1555 1555 2.82 LINK OD2 ASP A 24 CA CA A 128 1555 1555 2.88 LINK OE1 GLU A 27 CA CA A 128 1555 1555 2.74 LINK OE2 GLU A 27 CA CA A 128 1555 1555 2.80 LINK O ASP A 37 CA CA A 127 1555 1555 2.83 LINK OD1 ASP A 37 CA CA A 127 1555 1555 2.92 LINK O ASP A 38 CA CA A 127 1555 1555 2.89 LINK OD1 ASP A 38 CA CA A 127 1555 1555 2.91 LINK O LEU A 40 CA CA A 127 1555 1555 2.87 LINK OE2 GLU A 41 CA CA A 127 1555 1555 2.81 CISPEP 1 PHE A 42 PRO A 43 1 -10.16 CISPEP 2 PHE A 42 PRO A 43 2 -10.30 CISPEP 3 PHE A 42 PRO A 43 3 -10.25 CISPEP 4 PHE A 42 PRO A 43 4 -1.65 CISPEP 5 PHE A 42 PRO A 43 5 -0.75 CISPEP 6 PHE A 42 PRO A 43 6 -2.54 CISPEP 7 PHE A 42 PRO A 43 7 -10.15 CISPEP 8 PHE A 42 PRO A 43 8 1.62 CISPEP 9 PHE A 42 PRO A 43 9 -10.31 CISPEP 10 PHE A 42 PRO A 43 10 -0.46 CISPEP 11 PHE A 42 PRO A 43 11 -1.07 CISPEP 12 PHE A 42 PRO A 43 12 0.66 CISPEP 13 PHE A 42 PRO A 43 13 -0.37 CISPEP 14 PHE A 42 PRO A 43 14 0.42 CISPEP 15 PHE A 42 PRO A 43 15 0.69 CISPEP 16 PHE A 42 PRO A 43 16 -6.49 CISPEP 17 PHE A 42 PRO A 43 17 -0.99 CISPEP 18 PHE A 42 PRO A 43 18 0.07 CISPEP 19 PHE A 42 PRO A 43 19 -2.36 CISPEP 20 PHE A 42 PRO A 43 20 -10.16 SITE 1 AC1 2 ASP A 37 ASP A 38 SITE 1 AC2 3 ASP A 21 GLU A 23 ASP A 24 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