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
(ATOM LINES ARE NOT SHOWN.)
END
