PDB Short entry for 1RK9 HEADER METAL BINDING PROTEIN 21-NOV-03 1RK9 TITLE SOLUTION STRUCTURE OF HUMAN ALPHA-PARVALBUMIN (MINIMIZED AVERAGE TITLE 2 STRUCTURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARVALBUMIN ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-PARVALBUMIN; PARVALBUMIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CALCIUM, PARVALBUMIN, EF-HAND, LANTHANIDE, STRUCTURAL PROTEOMICS IN KEYWDS 2 EUROPE, SPINE, STRUCTURAL GENOMICS, METAL BINDING PROTEIN EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR I.BAIG,I.BERTINI,C.DEL BIANCO,Y.K.GUPTA,Y.-M.LEE,C.LUCHINAT, AUTHOR 2 A.QUATTRONE,STRUCTURAL PROTEOMICS IN EUROPE (SPINE) REVDAT 3 02-MAR-22 1RK9 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1RK9 1 VERSN REVDAT 1 08-JUN-04 1RK9 0 JRNL AUTH I.BAIG,I.BERTINI,C.DEL BIANCO,Y.K.GUPTA,Y.-M.LEE,C.LUCHINAT, JRNL AUTH 2 A.QUATTRONE JRNL TITL PARAMAGNETISM-BASED REFINEMENT STRATEGY FOR THE SOLUTION JRNL TITL 2 STRUCTURE OF HUMAN ALPHA-PARVALBUMIN JRNL REF BIOCHEMISTRY V. 43 5562 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15122922 JRNL DOI 10.1021/BI035879K REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, AMBER 5.0 REMARK 3 AUTHORS : BRUNGER (XWINNMR), REARLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020830. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 7.0; 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL; 100 MM REMARK 210 NACL; 100 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM PARVALBUMIN U-15N,13C; REMARK 210 100MM NACL; 90% H2O, 10% D2O; PH REMARK 210 7.0; FOR CACAPV; 0.6 MM REMARK 210 PARVALBUMIN U-15N; 100MM NACL; REMARK 210 90% H2O, 10% D2O; PH 7.0; FOR REMARK 210 CACAPV; 1.5 MM PARVALBUMIN U-15N, REMARK 210 13C; 100MM NACL; 90% H2O, 10% REMARK 210 D2O; PH 7.0; FOR CADYPV; 0.6 MM REMARK 210 PARVALBUMIN U-15N; 100MM NACL; REMARK 210 90% H2O, 10% D2O; PH 7.0; FOR REMARK 210 CADYPV REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D REMARK 210 TOCSY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, XEASY 1.3, DYANA REMARK 210 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY; SIMULATED REMARK 210 ANNEALING; MOLECULAR DYNAMICS; REMARK 210 TORSION ANGLE DYNAMICS REMARK 210 PSEUDOCONTACT SHIFTS; RESIDUE REMARK 210 DIPLOAR COUPLINGS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: REMARK 210 ALL SPECTROMETERS ARE EQUIPPED WITH A TRIPLE RESONANCE (TXI) 5 MM REMARK 210 PROBE WITH A Z-AXIS PULSE FIELD GRADIENT, AND THE 500 MHZ REMARK 210 SPECTROMETER REMARK 210 IS EQUIPPED WITH A TRIPLE RESONANCE CRYO-PROBE. THIS STRUCTURE WAS REMARK 210 DETERMINED USING PSEUDOCONTACT SHIFTS AND RESIDUE DIPOLAR COUPLINGS REMARK 210 WITH ALL DIAMAGNETIC RESTRAINTS 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 OD2 ASP A 23 HG SER A 79 1.33 REMARK 500 HG1 THR A 22 OD1 ASP A 23 1.36 REMARK 500 O GLU A 109 HG SER A 110 1.59 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 SER A 2 89.89 -164.77 REMARK 500 THR A 4 -57.12 -175.77 REMARK 500 ASN A 8 119.77 139.70 REMARK 500 SER A 24 35.46 -82.28 REMARK 500 LYS A 37 -16.43 -48.35 REMARK 500 PHE A 66 25.13 -146.96 REMARK 500 SER A 72 174.34 179.57 REMARK 500 ASP A 74 19.71 59.44 REMARK 500 ARG A 76 172.20 66.82 REMARK 500 LEU A 106 -45.94 -29.34 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 112 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 52 OD1 REMARK 620 2 ASP A 54 OD2 130.4 REMARK 620 3 ASP A 54 OD1 76.8 55.0 REMARK 620 4 SER A 56 OG 81.4 93.2 72.3 REMARK 620 5 PHE A 58 O 66.0 161.8 136.7 80.8 REMARK 620 6 GLU A 60 OE2 129.9 96.2 136.4 78.3 65.8 REMARK 620 7 GLU A 63 OE1 92.4 95.9 112.9 170.9 90.6 100.9 REMARK 620 8 GLU A 63 OE2 86.0 69.0 70.7 142.8 125.1 134.1 42.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 111 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 91 OD1 REMARK 620 2 ASP A 93 OD2 111.7 REMARK 620 3 ASP A 95 OD2 89.7 83.4 REMARK 620 4 LYS A 97 O 62.9 172.9 100.8 REMARK 620 5 GLU A 102 OE1 90.9 92.8 176.2 82.9 REMARK 620 6 GLU A 102 OE2 131.9 76.8 138.2 103.2 41.0 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 111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 112 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CIRMMP07 RELATED DB: TARGETDB DBREF 1RK9 A 2 110 UNP P20472 PRVA_HUMAN 1 109 SEQADV 1RK9 MET A 1 UNP P20472 INSERTION SEQRES 1 A 110 MET SER MET THR ASP LEU LEU ASN ALA GLU ASP ILE LYS SEQRES 2 A 110 LYS ALA VAL GLY ALA PHE SER ALA THR ASP SER PHE ASP SEQRES 3 A 110 HIS LYS LYS PHE PHE GLN MET VAL GLY LEU LYS LYS LYS SEQRES 4 A 110 SER ALA ASP ASP VAL LYS LYS VAL PHE HIS MET LEU ASP SEQRES 5 A 110 LYS ASP LYS SER GLY PHE ILE GLU GLU ASP GLU LEU GLY SEQRES 6 A 110 PHE ILE LEU LYS GLY PHE SER PRO ASP ALA ARG ASP LEU SEQRES 7 A 110 SER ALA LYS GLU THR LYS MET LEU MET ALA ALA GLY ASP SEQRES 8 A 110 LYS ASP GLY ASP GLY LYS ILE GLY VAL ASP GLU PHE SER SEQRES 9 A 110 THR LEU VAL ALA GLU SER HET CA A 111 1 HET CA A 112 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 ASN A 8 SER A 20 1 13 HELIX 2 2 ASP A 26 VAL A 34 1 9 HELIX 3 3 GLY A 35 LYS A 39 5 5 HELIX 4 4 SER A 40 ASP A 52 1 13 HELIX 5 5 GLU A 60 GLY A 65 1 6 HELIX 6 6 ILE A 67 SER A 72 1 6 HELIX 7 7 SER A 79 ASP A 91 1 13 HELIX 8 8 GLY A 99 SER A 110 1 12 LINK OD1 ASP A 52 CA CA A 112 1555 1555 3.01 LINK OD2 ASP A 54 CA CA A 112 1555 1555 2.19 LINK OD1 ASP A 54 CA CA A 112 1555 1555 2.39 LINK OG SER A 56 CA CA A 112 1555 1555 3.03 LINK O PHE A 58 CA CA A 112 1555 1555 2.50 LINK OE2 GLU A 60 CA CA A 112 1555 1555 2.99 LINK OE1 GLU A 63 CA CA A 112 1555 1555 2.41 LINK OE2 GLU A 63 CA CA A 112 1555 1555 3.25 LINK OD1 ASP A 91 CA CA A 111 1555 1555 3.04 LINK OD2 ASP A 93 CA CA A 111 1555 1555 3.02 LINK OD2 ASP A 95 CA CA A 111 1555 1555 2.12 LINK O LYS A 97 CA CA A 111 1555 1555 3.07 LINK OE1 GLU A 102 CA CA A 111 1555 1555 2.13 LINK OE2 GLU A 102 CA CA A 111 1555 1555 3.28 SITE 1 AC1 5 ASP A 91 ASP A 93 ASP A 95 LYS A 97 SITE 2 AC1 5 GLU A 102 SITE 1 AC2 6 ASP A 52 ASP A 54 SER A 56 PHE A 58 SITE 2 AC2 6 GLU A 60 GLU A 63 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