HEADER CALCIUM BINDING PROTEIN 25-MAY-10 2KYF TITLE SOLUTION STRUCTURE OF CALCIUM-BOUND CPV3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARVALBUMIN, THYMIC CPV3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARVALBUMIN-3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: BANTAM,CHICKENS; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET11 KEYWDS EF-HAND PROTEIN, PARVALBUMIN, CALCIUM BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.T.HENZL,J.J.TANNER,A.TAN REVDAT 3 14-JUN-23 2KYF 1 REMARK LINK REVDAT 2 05-FEB-20 2KYF 1 SEQADV REVDAT 1 06-APR-11 2KYF 0 JRNL AUTH M.T.HENZL,J.J.TANNER,A.TAN JRNL TITL SOLUTION STRUCTURES OF CHICKEN PARVALBUMIN 3 IN THE JRNL TITL 2 CA(2+)-FREE AND CA(2+)-BOUND STATES. JRNL REF PROTEINS V. 79 752 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21287610 JRNL DOI 10.1002/PROT.22915 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000101729. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.165 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.0 MM CA-BOUND CPV3, 150 MM REMARK 210 SODIUM CHLORIDE, 10 MM MES, 0.1 REMARK 210 MM CALCIUM CHLORIDE (FREE), 10 % REMARK 210 D2O, 0.1 % SODIUM AZIDE, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HN(CO)CA; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D C(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N TOCSY; 2D REMARK 210 HBCBCGCDHD; 2D HBCBCGCDCEHE; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 LEU A 2 -74.81 -52.29 REMARK 500 1 THR A 3 29.23 47.43 REMARK 500 1 ILE A 5 -66.17 -142.29 REMARK 500 1 ASP A 51 94.41 -68.15 REMARK 500 1 GLU A 59 172.80 -55.21 REMARK 500 1 ASP A 90 -72.60 -59.19 REMARK 500 1 HIS A 91 10.66 58.93 REMARK 500 1 PHE A 102 -62.18 -91.80 REMARK 500 1 VAL A 106 -78.25 -85.28 REMARK 500 2 LEU A 2 -75.96 -84.96 REMARK 500 2 THR A 3 27.25 48.69 REMARK 500 2 ILE A 5 -46.59 -140.85 REMARK 500 2 SER A 33 -69.09 -94.69 REMARK 500 2 GLU A 59 174.48 -56.31 REMARK 500 2 TYR A 65 43.72 -94.66 REMARK 500 2 VAL A 76 -166.69 -106.68 REMARK 500 2 ALA A 89 -55.90 -120.44 REMARK 500 2 ASP A 90 -72.06 -63.41 REMARK 500 2 PHE A 102 -69.40 -94.01 REMARK 500 2 VAL A 106 -78.66 -84.22 REMARK 500 3 LEU A 2 -74.71 -85.65 REMARK 500 3 THR A 3 29.75 48.40 REMARK 500 3 ILE A 5 -67.18 -143.23 REMARK 500 3 ALA A 74 174.67 -59.41 REMARK 500 3 ARG A 75 -174.09 -69.19 REMARK 500 3 GLU A 81 -60.68 -98.53 REMARK 500 3 ASP A 90 -71.75 -59.06 REMARK 500 3 VAL A 106 -77.59 -80.61 REMARK 500 4 LEU A 2 -75.72 69.42 REMARK 500 4 ALA A 20 150.60 -49.18 REMARK 500 4 SER A 33 -68.87 -99.06 REMARK 500 4 GLU A 81 -61.34 -96.21 REMARK 500 4 HIS A 91 17.21 55.39 REMARK 500 4 VAL A 106 -78.74 -83.08 REMARK 500 5 LEU A 2 -74.85 -84.29 REMARK 500 5 ILE A 5 -67.83 -142.58 REMARK 500 5 SER A 33 -64.36 -90.14 REMARK 500 5 TYR A 65 48.07 -100.26 REMARK 500 5 SER A 72 65.80 63.56 REMARK 500 5 ALA A 74 -176.24 -65.40 REMARK 500 5 GLU A 81 -61.51 -95.02 REMARK 500 5 HIS A 91 14.84 54.71 REMARK 500 5 VAL A 106 -77.71 -79.89 REMARK 500 6 LEU A 2 -73.23 -52.19 REMARK 500 6 THR A 3 29.17 48.37 REMARK 500 6 ILE A 5 -40.62 -139.98 REMARK 500 6 CYS A 18 40.84 -141.54 REMARK 500 6 ALA A 74 176.74 -55.89 REMARK 500 6 ARG A 75 -174.92 -69.34 REMARK 500 6 VAL A 76 -168.00 -109.58 REMARK 500 REMARK 500 THIS ENTRY HAS 180 RAMACHANDRAN OUTLIERS. 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 OD2 132.2 REMARK 620 3 SER A 55 OG 96.2 101.4 REMARK 620 4 PHE A 57 O 78.8 138.3 101.4 REMARK 620 5 GLU A 59 OE2 165.3 62.1 75.2 91.1 REMARK 620 6 GLU A 62 OE2 123.9 68.5 134.7 70.6 60.9 REMARK 620 7 GLU A 62 OE1 86.3 65.8 163.6 94.9 105.4 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 110 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD2 REMARK 620 2 ASP A 90 OD1 14.4 REMARK 620 3 ASP A 92 OD2 66.2 78.0 REMARK 620 4 ASP A 94 OD2 69.2 77.5 84.0 REMARK 620 5 LYS A 96 O 88.8 74.6 142.3 114.1 REMARK 620 6 GLU A 101 OE2 90.5 83.2 85.4 159.5 66.3 REMARK 620 7 GLU A 101 OE1 113.6 117.1 59.1 133.0 112.9 52.2 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 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 110 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KYC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF CA-FREE CHICKEN PARVALBUMIN 3 (CPV3) REMARK 900 RELATED ID: 16955 RELATED DB: BMRB DBREF 2KYF A 1 108 UNP P43305 PRVU_CHICK 2 109 SEQADV 2KYF SER A 72 UNP P43305 CYS 73 ENGINEERED MUTATION SEQRES 1 A 108 SER LEU THR ASP ILE LEU SER PRO SER ASP ILE ALA ALA SEQRES 2 A 108 ALA LEU ARG ASP CYS GLN ALA PRO ASP SER PHE SER PRO SEQRES 3 A 108 LYS LYS PHE PHE GLN ILE SER GLY MET SER LYS LYS SER SEQRES 4 A 108 SER SER GLN LEU LYS GLU ILE PHE ARG ILE LEU ASP ASN SEQRES 5 A 108 ASP GLN SER GLY PHE ILE GLU GLU ASP GLU LEU LYS TYR SEQRES 6 A 108 PHE LEU GLN ARG PHE GLU SER GLY ALA ARG VAL LEU THR SEQRES 7 A 108 ALA SER GLU THR LYS THR PHE LEU ALA ALA ALA ASP HIS SEQRES 8 A 108 ASP GLY ASP GLY LYS ILE GLY ALA GLU GLU PHE GLN GLU SEQRES 9 A 108 MET VAL GLN SER HET CA A 109 1 HET CA A 110 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 SER A 7 CYS A 18 1 12 HELIX 2 2 LEU A 43 ASP A 51 1 9 HELIX 3 3 GLU A 60 LYS A 64 1 5 HELIX 4 4 PHE A 66 GLU A 71 1 6 HELIX 5 5 GLU A 81 ASP A 90 1 10 HELIX 6 6 PHE A 102 SER A 108 1 7 SHEET 1 A 2 ILE A 58 GLU A 59 0 SHEET 2 A 2 LYS A 96 ILE A 97 -1 O ILE A 97 N ILE A 58 LINK OD1 ASP A 51 CA CA A 109 1555 1555 2.20 LINK OD2 ASP A 53 CA CA A 109 1555 1555 2.41 LINK OG SER A 55 CA CA A 109 1555 1555 2.72 LINK O PHE A 57 CA CA A 109 1555 1555 2.45 LINK OE2 GLU A 59 CA CA A 109 1555 1555 2.59 LINK OE2 GLU A 62 CA CA A 109 1555 1555 2.22 LINK OE1 GLU A 62 CA CA A 109 1555 1555 2.68 LINK OD2 ASP A 90 CA CA A 110 1555 1555 4.31 LINK OD1 ASP A 90 CA CA A 110 1555 1555 2.20 LINK OD2 ASP A 92 CA CA A 110 1555 1555 2.50 LINK OD2 ASP A 94 CA CA A 110 1555 1555 2.49 LINK O LYS A 96 CA CA A 110 1555 1555 2.66 LINK OE2 GLU A 101 CA CA A 110 1555 1555 2.27 LINK OE1 GLU A 101 CA CA A 110 1555 1555 2.66 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 5 ASP A 90 ASP A 92 ASP A 94 LYS A 96 SITE 2 AC2 5 GLU A 101 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20