PDB Short entry for 1TTX HEADER METAL BINDING PROTEIN 23-JUN-04 1TTX TITLE SOLUTION STRUCTURE OF HUMAN BETA PARVALBUMIN (ONCOMODULIN) REFINED TITLE 2 WITH A PARAMAGNETISM BASED STRATEGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ONCOMODULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA PARVALBUMIN, OM; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: XL1BLUE CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30XA KEYWDS ONCOMODULIN, EF-HAND, LANTHANIDE, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 PROTEOMICS IN EUROPE, SPINE, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.BABINI,I.BERTINI,F.CAPOZZI,C.DEL BIANCO,D.HOLLENDER,T.KISS, AUTHOR 2 C.LUCHINAT,A.QUATTRONE,STRUCTURAL PROTEOMICS IN EUROPE (SPINE) REVDAT 4 10-NOV-21 1TTX 1 REMARK SEQADV LINK REVDAT 3 28-DEC-16 1TTX 1 TITLE VERSN REVDAT 2 24-FEB-09 1TTX 1 VERSN REVDAT 1 18-JAN-05 1TTX 0 JRNL AUTH E.BABINI,I.BERTINI,F.CAPOZZI,C.DEL BIANCO,D.HOLLENDER, JRNL AUTH 2 T.KISS,C.LUCHINAT,A.QUATTRONE JRNL TITL SOLUTION STRUCTURE OF HUMAN BETA-PARVALBUMIN AND STRUCTURAL JRNL TITL 2 COMPARISON WITH ITS PARALOG ALPHA-PARVALBUMIN AND WITH THEIR JRNL TITL 3 RAT ORTHOLOGS(,) JRNL REF BIOCHEMISTRY V. 43 16076 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15610002 JRNL DOI 10.1021/BI048388O REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.1, AMBER 5 REMARK 3 AUTHORS : BRUNGER (XWINNMR), PEARLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TTX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022897. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 4MM PROTEIN U-15N-13C; 100MM REMARK 210 NACL; PH 6.5; 4MM PROTEIN U-15N; REMARK 210 100MM NACL; PH 6.5; 4MM PROTEIN REMARK 210 UNLABELED; 100MM NACL; PH 6.5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, SPARKY 3, DYANA 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING TORSION ANGLE DYNAMICS; REMARK 210 PSEUDOCONTACT SHIFTS RESIDUAL REMARK 210 DIPOLAR COUPLINGS; REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: THE STRUCTURE WAS DETERMINED USING DIAMAGNETIC CONSTRAINTS REMARK 210 PLUS PSEUDOCONTACT SHIFTS AND RESIDUAL DIPOLAR COUPLING 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 5 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ASP A 52 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 15 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 19 ASP A 52 CB - CG - OD2 ANGL. DEV. = 6.0 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 SER A 2 -66.92 -161.95 REMARK 500 1 LEU A 7 -58.80 173.24 REMARK 500 1 CYS A 19 62.55 -106.92 REMARK 500 1 ASP A 23 37.62 74.40 REMARK 500 1 GLN A 55 12.64 59.64 REMARK 500 1 TYR A 58 143.71 -171.05 REMARK 500 1 LEU A 59 68.54 -102.93 REMARK 500 1 ASN A 92 41.31 -76.26 REMARK 500 1 ASP A 93 -58.98 -126.11 REMARK 500 2 SER A 2 -66.92 -161.95 REMARK 500 2 LEU A 7 -58.80 173.24 REMARK 500 2 CYS A 19 62.55 -106.92 REMARK 500 2 ASP A 23 37.62 74.40 REMARK 500 2 GLN A 55 12.64 59.64 REMARK 500 2 TYR A 58 143.71 -171.05 REMARK 500 2 LEU A 59 68.54 -102.93 REMARK 500 2 ASN A 92 41.31 -76.26 REMARK 500 2 ASP A 93 -58.98 -126.11 REMARK 500 3 ASP A 5 44.34 -153.11 REMARK 500 3 VAL A 6 -59.14 -128.29 REMARK 500 3 LEU A 7 -47.55 -172.54 REMARK 500 3 PRO A 27 -73.34 -65.70 REMARK 500 3 GLN A 55 72.09 53.87 REMARK 500 3 PHE A 67 -74.63 -66.06 REMARK 500 3 PHE A 71 -62.70 -94.07 REMARK 500 3 ALA A 75 -142.41 -91.10 REMARK 500 3 ASN A 92 45.48 -76.19 REMARK 500 3 ASP A 93 -58.93 -135.37 REMARK 500 3 ASP A 95 -61.89 -124.60 REMARK 500 4 SER A 2 -72.24 157.74 REMARK 500 4 VAL A 6 -61.82 -121.02 REMARK 500 4 LEU A 7 -61.55 -171.95 REMARK 500 4 SER A 8 -37.83 -33.03 REMARK 500 4 SER A 40 139.93 113.99 REMARK 500 4 ASP A 52 -49.04 -155.99 REMARK 500 4 ASN A 53 -52.88 97.62 REMARK 500 4 ALA A 75 -165.85 -71.42 REMARK 500 4 GLU A 77 -6.90 -59.35 REMARK 500 4 ASP A 95 -55.03 -121.94 REMARK 500 5 ASP A 5 -50.89 -174.64 REMARK 500 5 LEU A 7 -58.47 -164.34 REMARK 500 5 ASP A 52 75.57 -66.98 REMARK 500 5 ASP A 54 -44.77 72.23 REMARK 500 5 SER A 56 -6.98 -57.78 REMARK 500 5 PHE A 66 30.28 -152.80 REMARK 500 5 GLN A 69 14.06 -69.50 REMARK 500 5 ASP A 95 -50.63 -134.74 REMARK 500 6 SER A 2 -82.17 143.90 REMARK 500 6 VAL A 6 -64.40 -120.05 REMARK 500 6 LEU A 7 -54.45 -169.89 REMARK 500 REMARK 500 THIS ENTRY HAS 213 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 PHE A 50 0.09 SIDE CHAIN REMARK 500 2 PHE A 50 0.09 SIDE CHAIN REMARK 500 3 ARG A 20 0.08 SIDE CHAIN REMARK 500 3 PHE A 71 0.08 SIDE CHAIN REMARK 500 5 PHE A 25 0.14 SIDE CHAIN REMARK 500 7 ARG A 76 0.12 SIDE CHAIN REMARK 500 8 ARG A 76 0.15 SIDE CHAIN REMARK 500 9 PHE A 48 0.10 SIDE CHAIN REMARK 500 9 ARG A 76 0.09 SIDE CHAIN REMARK 500 10 ARG A 76 0.18 SIDE CHAIN REMARK 500 11 PHE A 25 0.08 SIDE CHAIN REMARK 500 11 PHE A 48 0.10 SIDE CHAIN REMARK 500 11 ARG A 76 0.10 SIDE CHAIN REMARK 500 12 PHE A 48 0.10 SIDE CHAIN REMARK 500 12 PHE A 71 0.10 SIDE CHAIN REMARK 500 14 ARG A 76 0.10 SIDE CHAIN REMARK 500 14 PHE A 103 0.08 SIDE CHAIN REMARK 500 15 PHE A 25 0.13 SIDE CHAIN REMARK 500 15 TYR A 58 0.08 SIDE CHAIN REMARK 500 15 PHE A 67 0.14 SIDE CHAIN REMARK 500 18 PHE A 48 0.12 SIDE CHAIN REMARK 500 18 TYR A 58 0.07 SIDE CHAIN REMARK 500 19 TYR A 58 0.07 SIDE CHAIN REMARK 500 20 PHE A 71 0.08 SIDE CHAIN REMARK 500 20 ARG A 76 0.17 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 111 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 52 OD1 REMARK 620 2 ASP A 52 OD2 54.9 REMARK 620 3 SER A 56 OG 108.4 108.7 REMARK 620 4 TYR A 58 O 122.0 76.4 116.2 REMARK 620 5 GLU A 63 OE1 100.0 123.0 128.3 80.3 REMARK 620 6 GLU A 63 OE2 112.7 167.5 72.3 114.8 56.9 REMARK 620 N 1 2 3 4 5 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 91 OD1 REMARK 620 2 ASP A 93 OD1 126.4 REMARK 620 3 ASP A 93 OD2 133.9 7.5 REMARK 620 4 ASP A 95 OD2 110.7 73.8 72.5 REMARK 620 5 ASP A 95 OD1 74.4 88.4 91.4 37.4 REMARK 620 6 LYS A 97 O 86.4 142.4 136.2 77.7 83.4 REMARK 620 7 GLU A 102 OE1 90.0 86.4 86.3 157.2 155.9 114.4 REMARK 620 8 GLU A 102 OE2 125.6 94.6 88.5 114.5 149.0 75.5 55.0 REMARK 620 N 1 2 3 4 5 6 7 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 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 111 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CIRMMP08 RELATED DB: TARGETDB DBREF 1TTX A 1 109 UNP P32930 ONCO_HUMAN 0 108 SEQADV 1TTX ARG A 20 UNP P32930 GLN 19 ENGINEERED MUTATION SEQRES 1 A 109 MET SER ILE THR ASP VAL LEU SER ALA ASP ASP ILE ALA SEQRES 2 A 109 ALA ALA LEU GLN GLU CYS ARG ASP PRO ASP THR PHE GLU SEQRES 3 A 109 PRO GLN LYS PHE PHE GLN THR SER GLY LEU SER LYS MET SEQRES 4 A 109 SER ALA ASN GLN VAL LYS ASP VAL PHE ARG PHE ILE ASP SEQRES 5 A 109 ASN ASP GLN SER GLY TYR LEU ASP GLU GLU GLU LEU LYS SEQRES 6 A 109 PHE PHE LEU GLN LYS PHE GLU SER GLY ALA ARG GLU LEU SEQRES 7 A 109 THR GLU SER GLU THR LYS SER LEU MET ALA ALA ALA ASP SEQRES 8 A 109 ASN ASP GLY ASP GLY LYS ILE GLY ALA GLU GLU PHE GLN SEQRES 9 A 109 GLU MET VAL HIS SER HET CA A 110 1 HET CA A 111 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 LEU A 7 CYS A 19 1 13 HELIX 2 2 GLU A 26 SER A 34 1 9 HELIX 3 3 SER A 40 ASP A 52 1 13 HELIX 4 4 ASP A 60 LYS A 65 1 6 HELIX 5 5 PHE A 66 PHE A 71 5 6 HELIX 6 6 THR A 79 ASP A 91 1 13 HELIX 7 7 GLY A 99 SER A 109 1 11 LINK OD1 ASP A 52 CA CA A 111 1555 1555 2.26 LINK OD2 ASP A 52 CA CA A 111 1555 1555 2.34 LINK OG SER A 56 CA CA A 111 1555 1555 2.30 LINK O TYR A 58 CA CA A 111 1555 1555 2.27 LINK OE1 GLU A 63 CA CA A 111 1555 1555 2.22 LINK OE2 GLU A 63 CA CA A 111 1555 1555 2.28 LINK OD1 ASP A 91 CA CA A 110 1555 1555 2.21 LINK OD1 ASP A 93 CA CA A 110 1555 1555 4.39 LINK OD2 ASP A 93 CA CA A 110 1555 1555 2.20 LINK OD2 ASP A 95 CA CA A 110 1555 1555 3.48 LINK OD1 ASP A 95 CA CA A 110 1555 1555 2.23 LINK O LYS A 97 CA CA A 110 1555 1555 2.34 LINK OE1 GLU A 102 CA CA A 110 1555 1555 2.26 LINK OE2 GLU A 102 CA CA A 110 1555 1555 2.37 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 4 ASP A 52 SER A 56 TYR A 58 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