HEADER METAL TRANSPORT 21-APR-06 2GQL TITLE SOLUTION STRUCTURE OF HUMAN NI(II)-SCO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCO1 PROTEIN HOMOLOG, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (RESIDUES 132-301); 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 GENE: SCO1, SCOD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3 GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETG-30A KEYWDS THIOREDOXIN-LIKE FOLD, METALLOPROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL PROTEOMICS IN EUROPE, SPINE, METAL TRANSPORT EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR L.BANCI,I.BERTINI,V.CALDERONE,S.CIOFI-BAFFONI,S.MANGANI,P.PALUMAA, AUTHOR 2 M.MARTINELLI,S.WANG,STRUCTURAL PROTEOMICS IN EUROPE (SPINE) REVDAT 4 09-MAR-22 2GQL 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2GQL 1 VERSN REVDAT 2 20-JUN-06 2GQL 1 JRNL REVDAT 1 06-JUN-06 2GQL 0 JRNL AUTH L.BANCI,I.BERTINI,V.CALDERONE,S.CIOFI-BAFFONI,S.MANGANI, JRNL AUTH 2 M.MARTINELLI,P.PALUMAA,S.WANG JRNL TITL A HINT FOR THE FUNCTION OF HUMAN SCO1 FROM DIFFERENT JRNL TITL 2 STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 8595 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16735468 JRNL DOI 10.1073/PNAS.0601375103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 8.0 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GQL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037433. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM HUMAN NI(II) SCO1 U-15N, REMARK 210 13C, 50MM PHOSPHATE BUFFER NA, REMARK 210 1MM DTT, 90% H2O, 10% D2O; 1MM REMARK 210 HUMAN NI(II) SCO1 U-15N, 50MM REMARK 210 PHOSPHATE BUFFER NA, 1MM DTT, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; REMARK 210 CBCA(CO)NH; HNCA; HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, CARA 2.1, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 HG1 THR A 151 OD1 ASP A 154 1.58 REMARK 500 HG SER A 141 OE2 GLU A 233 1.59 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 CYS A 169 CB - CA - C ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 3.2 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 PHE A 130 -163.12 -63.22 REMARK 500 LEU A 135 44.44 -79.17 REMARK 500 GLN A 158 -166.06 -111.96 REMARK 500 PRO A 170 47.44 -90.67 REMARK 500 ASP A 171 -66.01 -122.92 REMARK 500 THR A 191 -18.98 64.79 REMARK 500 ARG A 207 -48.65 -174.25 REMARK 500 ASP A 208 91.83 -64.06 REMARK 500 SER A 221 139.17 -171.57 REMARK 500 GLU A 252 -116.54 -98.84 REMARK 500 ASP A 270 -19.82 70.33 REMARK 500 LEU A 274 -31.74 -131.64 REMARK 500 PHE A 277 -163.03 -100.03 REMARK 500 ASN A 280 -37.42 88.77 REMARK 500 LYS A 300 -7.10 -156.28 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 THR A 261 ILE A 262 -143.11 REMARK 500 LYS A 300 SER A 301 -108.55 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 ARG A 231 0.08 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 NI A 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 166 O REMARK 620 2 CYS A 169 O 101.1 REMARK 620 3 CYS A 169 SG 93.0 88.6 REMARK 620 4 CYS A 173 SG 85.7 99.9 171.5 REMARK 620 5 HIS A 260 NE2 110.6 148.2 87.7 84.9 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 NI A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GQK RELATED DB: PDB REMARK 900 FAMILY OF 30 STRUCTURES OF HUMAN NI(II)-SCO1 REMARK 900 RELATED ID: CIRMMP13 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2GQM RELATED DB: PDB DBREF 2GQL A 132 301 UNP O75880 SCO1_HUMAN 132 301 SEQADV 2GQL SER A 129 UNP O75880 CLONING ARTIFACT SEQADV 2GQL PHE A 130 UNP O75880 CLONING ARTIFACT SEQADV 2GQL THR A 131 UNP O75880 CLONING ARTIFACT SEQRES 1 A 173 SER PHE THR GLY LYS PRO LEU LEU GLY GLY PRO PHE SER SEQRES 2 A 173 LEU THR THR HIS THR GLY GLU ARG LYS THR ASP LYS ASP SEQRES 3 A 173 TYR LEU GLY GLN TRP LEU LEU ILE TYR PHE GLY PHE THR SEQRES 4 A 173 HIS CYS PRO ASP VAL CYS PRO GLU GLU LEU GLU LYS MET SEQRES 5 A 173 ILE GLN VAL VAL ASP GLU ILE ASP SER ILE THR THR LEU SEQRES 6 A 173 PRO ASP LEU THR PRO LEU PHE ILE SER ILE ASP PRO GLU SEQRES 7 A 173 ARG ASP THR LYS GLU ALA ILE ALA ASN TYR VAL LYS GLU SEQRES 8 A 173 PHE SER PRO LYS LEU VAL GLY LEU THR GLY THR ARG GLU SEQRES 9 A 173 GLU VAL ASP GLN VAL ALA ARG ALA TYR ARG VAL TYR TYR SEQRES 10 A 173 SER PRO GLY PRO LYS ASP GLU ASP GLU ASP TYR ILE VAL SEQRES 11 A 173 ASP HIS THR ILE ILE MET TYR LEU ILE GLY PRO ASP GLY SEQRES 12 A 173 GLU PHE LEU ASP TYR PHE GLY GLN ASN LYS ARG LYS GLY SEQRES 13 A 173 GLU ILE ALA ALA SER ILE ALA THR HIS MET ARG PRO TYR SEQRES 14 A 173 ARG LYS LYS SER HET NI A 302 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ HELIX 1 1 ASP A 171 SER A 189 1 19 HELIX 2 2 THR A 209 SER A 221 1 13 HELIX 3 3 THR A 230 ARG A 242 1 13 HELIX 4 4 PRO A 269 GLY A 271 5 3 HELIX 5 5 ARG A 282 MET A 294 1 13 SHEET 1 A 6 THR A 143 THR A 144 0 SHEET 2 A 6 VAL A 225 THR A 228 -1 O THR A 228 N THR A 143 SHEET 3 A 6 LEU A 196 SER A 202 1 N PHE A 200 O LEU A 227 SHEET 4 A 6 TRP A 159 GLY A 165 1 N GLY A 165 O ILE A 201 SHEET 5 A 6 ILE A 263 ILE A 267 -1 O TYR A 265 N ILE A 162 SHEET 6 A 6 PHE A 273 GLY A 278 -1 O PHE A 277 N MET A 264 SHEET 1 B 2 SER A 246 PRO A 247 0 SHEET 2 B 2 VAL A 258 ASP A 259 -1 O ASP A 259 N SER A 246 LINK O PHE A 166 NI NI A 302 1555 1555 1.97 LINK O CYS A 169 NI NI A 302 1555 1555 1.92 LINK SG CYS A 169 NI NI A 302 1555 1555 2.45 LINK SG CYS A 173 NI NI A 302 1555 1555 2.56 LINK NE2 HIS A 260 NI NI A 302 1555 1555 2.23 CISPEP 1 SER A 129 PHE A 130 0 -6.53 CISPEP 2 PHE A 130 THR A 131 0 -0.78 SITE 1 AC1 4 PHE A 166 CYS A 169 CYS A 173 HIS A 260 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