HEADER CHAPERONE 24-MAR-06 2GGT TITLE CRYSTAL STRUCTURE OF HUMAN SCO1 COMPLEXED WITH NICKEL. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCO1 PROTEIN HOMOLOG, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COPPER CHAPERONE, CU-BINDING PROTEIN, MITOCHONDRIAL ASSEMBLY FACTOR, KEYWDS 2 REDOX, NICKEL, DISUPLHIDE, MITOCHONDRION, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR L.BANCI,I.BERTINI,V.CALDERONE,S.CIOFI-BAFFONI,S.MANGANI,M.MARTINELLI, AUTHOR 2 P.PALUMAA,S.WANG REVDAT 4 30-AUG-23 2GGT 1 REMARK LINK REVDAT 3 24-FEB-09 2GGT 1 VERSN REVDAT 2 12-FEB-08 2GGT 1 JRNL REVDAT 1 16-MAY-06 2GGT 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.C.WILLIAMS,C.SUE,G.S.BANTING,H.YANG,D.M.GLERUM, REMARK 1 AUTH 2 W.A.HENDRICKSON,E.A.SCHON REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN SCO1: IMPLICATIONS FOR REDOX REMARK 1 TITL 2 SIGNALING BY A MITOCHONDRIAL CYTOCHROME C OXIDASE 'ASSEMBLY' REMARK 1 TITL 3 PROTEIN. REMARK 1 REF J.BIOL.CHEM. V. 280 15202 2005 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15659396 REMARK 1 DOI 10.1074/JBC.M410705200 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.BALATRI,L.BANCI,I.BERTINI,F.CANTINI,S.CIOFI-BAFFONI REMARK 1 TITL SOLUTION STRUCTURE OF SCO1: A THIOREDOXIN-LIKE PROTEIN REMARK 1 TITL 2 INVOLVED IN CYTOCHROME C OXIDASE ASSEMBLY. REMARK 1 REF STRUCTURE V. 11 1431 2003 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 14604533 REMARK 1 DOI 10.1016/J.STR.2003.10.004 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13358 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1328 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 724 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.548 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.353 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2698 ; 0.037 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3668 ; 2.920 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ;10.853 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;37.596 ;24.264 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 453 ;23.630 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;24.215 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 401 ; 0.225 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2073 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1292 ; 0.292 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1708 ; 0.330 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.237 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.158 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 34 ; 0.274 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.069 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1705 ; 1.576 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2662 ; 2.581 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1171 ; 3.931 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1006 ; 5.494 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000037099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SILICON REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : CHANNEL-CUT SILICON REMARK 200 MONOCHROMATOR AND CYLINDRICAL REMARK 200 GRAZING INCIDENCE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14686 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 78.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : 0.45500 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1WP0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 TRIS-HCL, 25% PEG6000, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.73050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.20550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.22200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.20550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.73050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.22200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE PROTEIN IS MONOMERIC IN VIVO BUT THERE ARE TWO REMARK 300 MOLECULES IN THE ASYMMETRIC UNIT. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG B 298 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O GLU B 254 O HOH B 65 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 169 CB CYS A 169 SG 0.131 REMARK 500 CYS A 173 CB CYS A 173 SG 0.112 REMARK 500 GLU A 175 CB GLU A 175 CG 0.119 REMARK 500 GLU A 175 CG GLU A 175 CD 0.102 REMARK 500 GLU A 175 CD GLU A 175 OE2 0.071 REMARK 500 GLU A 186 CG GLU A 186 CD 0.100 REMARK 500 GLU A 219 CG GLU A 219 CD 0.119 REMARK 500 GLU A 219 CD GLU A 219 OE2 0.076 REMARK 500 GLU A 232 CD GLU A 232 OE2 0.077 REMARK 500 ILE A 257 CB ILE A 257 CG2 0.200 REMARK 500 GLY A 268 C GLY A 268 O 0.102 REMARK 500 PHE A 273 CE1 PHE A 273 CZ 0.153 REMARK 500 ARG A 298 CZ ARG A 298 NH1 0.089 REMARK 500 GLY B 137 CA GLY B 137 C 0.099 REMARK 500 VAL B 183 CB VAL B 183 CG2 -0.133 REMARK 500 GLU B 186 CD GLU B 186 OE1 0.081 REMARK 500 GLU B 232 CG GLU B 232 CD 0.103 REMARK 500 ASP B 253 C GLU B 254 N 0.295 REMARK 500 GLU B 254 C ASP B 255 N 0.213 REMARK 500 ASP B 270 CB ASP B 270 CG 0.147 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 ASP A 152 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU A 161 CB - CG - CD2 ANGL. DEV. = -14.4 DEGREES REMARK 500 MET A 294 CG - SD - CE ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG A 298 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 298 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 LEU B 136 CB - CG - CD1 ANGL. DEV. = 16.3 DEGREES REMARK 500 PRO B 222 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 LEU B 227 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 VAL B 237 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 PRO B 249 C - N - CA ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP B 253 CA - C - N ANGL. DEV. = -16.2 DEGREES REMARK 500 ASP B 253 O - C - N ANGL. DEV. = 13.3 DEGREES REMARK 500 GLU B 254 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 295 NE - CZ - NH2 ANGL. DEV. = 5.6 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 HIS A 168 26.59 -77.08 REMARK 500 SER A 189 -73.36 -38.03 REMARK 500 ASP A 208 58.63 -96.75 REMARK 500 GLN A 236 -65.56 -23.97 REMARK 500 SER A 246 102.69 -161.73 REMARK 500 PRO A 249 147.12 -39.53 REMARK 500 GLU A 252 -62.25 2.10 REMARK 500 GLU A 254 -14.99 78.97 REMARK 500 GLU A 285 -75.92 -50.17 REMARK 500 LEU B 136 59.10 -161.07 REMARK 500 PHE B 166 118.36 160.07 REMARK 500 THR B 167 -33.28 -35.67 REMARK 500 PRO B 170 -74.87 -59.38 REMARK 500 ASP B 171 -69.63 -97.49 REMARK 500 GLU B 178 -72.73 -38.58 REMARK 500 PRO B 194 172.01 -46.18 REMARK 500 LYS B 210 -82.47 -2.76 REMARK 500 PHE B 220 -50.73 -124.62 REMARK 500 SER B 221 149.52 158.06 REMARK 500 PRO B 222 3.71 -52.06 REMARK 500 TYR B 245 98.71 -161.81 REMARK 500 PRO B 249 122.88 -22.27 REMARK 500 ASP B 253 -59.47 155.77 REMARK 500 GLU B 254 58.96 109.69 REMARK 500 ILE B 262 44.28 -106.79 REMARK 500 PRO B 296 -108.34 -40.86 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 ILE A 190 THR A 191 -148.11 REMARK 500 LEU B 136 GLY B 137 139.84 REMARK 500 LEU B 227 THR B 228 149.09 REMARK 500 PHE B 277 GLY B 278 130.75 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 299 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 169 SG REMARK 620 2 CYS A 173 SG 66.4 REMARK 620 3 HIS A 260 NE2 163.0 99.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 299 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 169 SG REMARK 620 2 CYS B 173 SG 62.5 REMARK 620 3 HIS B 260 NE2 141.3 84.8 REMARK 620 N 1 2 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 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 299 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WP0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO HUMAN SCO1. REMARK 900 RELATED ID: 1ON4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF SOLUBLE DOMAIN OF SCO1 FROM BACILLUS SUBTILIS. DBREF 2GGT A 135 298 UNP O75880 SCO1_HUMAN 135 298 DBREF 2GGT B 135 298 UNP O75880 SCO1_HUMAN 135 298 SEQRES 1 A 164 LEU LEU GLY GLY PRO PHE SER LEU THR THR HIS THR GLY SEQRES 2 A 164 GLU ARG LYS THR ASP LYS ASP TYR LEU GLY GLN TRP LEU SEQRES 3 A 164 LEU ILE TYR PHE GLY PHE THR HIS CYS PRO ASP VAL CYS SEQRES 4 A 164 PRO GLU GLU LEU GLU LYS MET ILE GLN VAL VAL ASP GLU SEQRES 5 A 164 ILE ASP SER ILE THR THR LEU PRO ASP LEU THR PRO LEU SEQRES 6 A 164 PHE ILE SER ILE ASP PRO GLU ARG ASP THR LYS GLU ALA SEQRES 7 A 164 ILE ALA ASN TYR VAL LYS GLU PHE SER PRO LYS LEU VAL SEQRES 8 A 164 GLY LEU THR GLY THR ARG GLU GLU VAL ASP GLN VAL ALA SEQRES 9 A 164 ARG ALA TYR ARG VAL TYR TYR SER PRO GLY PRO LYS ASP SEQRES 10 A 164 GLU ASP GLU ASP TYR ILE VAL ASP HIS THR ILE ILE MET SEQRES 11 A 164 TYR LEU ILE GLY PRO ASP GLY GLU PHE LEU ASP TYR PHE SEQRES 12 A 164 GLY GLN ASN LYS ARG LYS GLY GLU ILE ALA ALA SER ILE SEQRES 13 A 164 ALA THR HIS MET ARG PRO TYR ARG SEQRES 1 B 164 LEU LEU GLY GLY PRO PHE SER LEU THR THR HIS THR GLY SEQRES 2 B 164 GLU ARG LYS THR ASP LYS ASP TYR LEU GLY GLN TRP LEU SEQRES 3 B 164 LEU ILE TYR PHE GLY PHE THR HIS CYS PRO ASP VAL CYS SEQRES 4 B 164 PRO GLU GLU LEU GLU LYS MET ILE GLN VAL VAL ASP GLU SEQRES 5 B 164 ILE ASP SER ILE THR THR LEU PRO ASP LEU THR PRO LEU SEQRES 6 B 164 PHE ILE SER ILE ASP PRO GLU ARG ASP THR LYS GLU ALA SEQRES 7 B 164 ILE ALA ASN TYR VAL LYS GLU PHE SER PRO LYS LEU VAL SEQRES 8 B 164 GLY LEU THR GLY THR ARG GLU GLU VAL ASP GLN VAL ALA SEQRES 9 B 164 ARG ALA TYR ARG VAL TYR TYR SER PRO GLY PRO LYS ASP SEQRES 10 B 164 GLU ASP GLU ASP TYR ILE VAL ASP HIS THR ILE ILE MET SEQRES 11 B 164 TYR LEU ILE GLY PRO ASP GLY GLU PHE LEU ASP TYR PHE SEQRES 12 B 164 GLY GLN ASN LYS ARG LYS GLY GLU ILE ALA ALA SER ILE SEQRES 13 B 164 ALA THR HIS MET ARG PRO TYR ARG HET NI A 299 1 HET CL A 300 1 HET NI B 299 1 HET CL B 301 1 HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION FORMUL 3 NI 2(NI 2+) FORMUL 4 CL 2(CL 1-) FORMUL 7 HOH *57(H2 O) HELIX 1 1 LYS A 153 LEU A 156 5 4 HELIX 2 2 ASP A 171 ILE A 190 1 20 HELIX 3 3 THR A 209 GLU A 219 1 11 HELIX 4 4 THR A 230 ALA A 240 1 11 HELIX 5 5 ARG A 282 ARG A 295 1 14 HELIX 6 6 PRO A 296 ARG A 298 5 3 HELIX 7 7 LYS B 153 LEU B 156 5 4 HELIX 8 8 ASP B 171 SER B 189 1 19 HELIX 9 9 THR B 209 VAL B 217 1 9 HELIX 10 10 THR B 230 TYR B 241 1 12 HELIX 11 11 ARG B 282 ARG B 295 1 14 SHEET 1 A 7 ARG A 149 THR A 151 0 SHEET 2 A 7 SER A 141 THR A 144 -1 N LEU A 142 O LYS A 150 SHEET 3 A 7 VAL A 225 THR A 228 -1 O THR A 228 N THR A 143 SHEET 4 A 7 LEU A 196 SER A 202 1 N PHE A 200 O VAL A 225 SHEET 5 A 7 TRP A 159 GLY A 165 1 N TRP A 159 O THR A 197 SHEET 6 A 7 ILE A 263 ILE A 267 -1 O ILE A 267 N LEU A 160 SHEET 7 A 7 PHE A 273 GLY A 278 -1 O LEU A 274 N LEU A 266 SHEET 1 B 2 TYR A 245 LYS A 250 0 SHEET 2 B 2 TYR A 256 HIS A 260 -1 O ILE A 257 N GLY A 248 SHEET 1 C 7 ARG B 149 THR B 151 0 SHEET 2 C 7 SER B 141 THR B 144 -1 N LEU B 142 O LYS B 150 SHEET 3 C 7 VAL B 225 THR B 228 -1 O THR B 228 N THR B 143 SHEET 4 C 7 THR B 197 SER B 202 1 N PHE B 200 O VAL B 225 SHEET 5 C 7 LEU B 160 GLY B 165 1 N LEU B 161 O THR B 197 SHEET 6 C 7 MET B 264 ILE B 267 -1 O ILE B 267 N LEU B 160 SHEET 7 C 7 PHE B 273 PHE B 277 -1 O LEU B 274 N LEU B 266 SHEET 1 D 2 TYR B 245 PRO B 247 0 SHEET 2 D 2 VAL B 258 HIS B 260 -1 O ASP B 259 N SER B 246 SSBOND 1 CYS A 169 CYS A 173 1555 1555 2.30 SSBOND 2 CYS B 169 CYS B 173 1555 1555 2.19 LINK SG CYS A 169 NI NI A 299 1555 1555 2.22 LINK SG CYS A 173 NI NI A 299 1555 1555 1.95 LINK NE2 HIS A 260 NI NI A 299 1555 1555 2.02 LINK SG CYS B 169 NI NI B 299 1555 1555 2.11 LINK SG CYS B 173 NI NI B 299 1555 1555 2.10 LINK NE2 HIS B 260 NI NI B 299 1555 1555 2.42 SITE 1 AC1 5 PHE A 166 CYS A 169 CYS A 173 HIS A 260 SITE 2 AC1 5 CL A 300 SITE 1 AC2 2 HIS A 260 NI A 299 SITE 1 AC3 4 CYS B 169 CYS B 173 HIS B 260 CL B 301 SITE 1 AC4 2 HIS B 260 NI B 299 CRYST1 51.461 52.444 136.411 90.00 90.00 90.00 P 21 21 21 8 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 0.019432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007331 0.00000