HEADER CHAPERONE 01-MAR-00 1EJ8 TITLE CRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR TITLE 2 SUPEROXIDE DISMUTASE (LYS7) AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYS7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COPPER CHAPERONE FOR YEAST SOD SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS BETA BARREL, COPPER CHAPERONE FOR SOD, DOMAIN 2, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR L.T.HALL,R.J.SANCHEZ,S.P.HOLLOWAY,H.ZHU,J.E.STINE,T.J.LYONS, AUTHOR 2 B.DEMELER,V.SCHIRF,J.C.HANSEN,A.M.NERSISSIAN,J.S.VALENTINE,P.J.HART REVDAT 4 07-FEB-24 1EJ8 1 REMARK LINK REVDAT 3 24-FEB-09 1EJ8 1 VERSN REVDAT 2 10-MAY-00 1EJ8 1 JRNL REVDAT 1 05-APR-00 1EJ8 0 JRNL AUTH L.T.HALL,R.J.SANCHEZ,S.P.HOLLOWAY,H.ZHU,J.E.STINE,T.J.LYONS, JRNL AUTH 2 B.DEMELER,V.SCHIRF,J.C.HANSEN,A.M.NERSISSIAN,J.S.VALENTINE, JRNL AUTH 3 P.J.HART JRNL TITL X-RAY CRYSTALLOGRAPHIC AND ANALYTICAL ULTRACENTRIFUGATION JRNL TITL 2 ANALYSES OF TRUNCATED AND FULL-LENGTH YEAST COPPER JRNL TITL 3 CHAPERONES FOR SOD (LYS7): A DIMER-DIMER MODEL OF LYS7-SOD JRNL TITL 4 ASSOCIATION AND COPPER DELIVERY. JRNL REF BIOCHEMISTRY V. 39 3611 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10736160 JRNL DOI 10.1021/BI992716G REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.196 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1719 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17564 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1081 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 2.200 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EJ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17203 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, CACL2, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 17.07700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.95350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.16300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.95350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.07700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.16300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 204 CB OG REMARK 470 SER A 205 CB OG REMARK 470 ARG A 217 CB CG CD NE CZ NH1 NH2 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 ARG A 105 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 TYR A 129 CG - CD1 - CE1 ANGL. DEV. = -4.8 DEGREES REMARK 500 LEU A 212 CA - CB - CG ANGL. DEV. = 17.7 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 GLU A 202 51.69 -166.59 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 218 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 124 O REMARK 620 2 ASN A 168 O 79.4 REMARK 620 3 ASN A 168 OD1 114.3 71.6 REMARK 620 4 HOH A1002 O 89.9 135.6 74.1 REMARK 620 5 HOH A1003 O 99.1 75.1 126.4 149.3 REMARK 620 6 HOH A1004 O 159.5 120.1 80.3 80.0 81.6 REMARK 620 7 HOH A1005 O 83.6 143.4 144.8 76.0 76.0 76.6 REMARK 620 N 1 2 3 4 5 6 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 218 DBREF 1EJ8 A 78 217 UNP P40202 CCS1_YEAST 78 217 SEQRES 1 A 140 SER SER ALA VAL ALA ILE LEU GLU THR PHE GLN LYS TYR SEQRES 2 A 140 THR ILE ASP GLN LYS LYS ASP THR ALA VAL ARG GLY LEU SEQRES 3 A 140 ALA ARG ILE VAL GLN VAL GLY GLU ASN LYS THR LEU PHE SEQRES 4 A 140 ASP ILE THR VAL ASN GLY VAL PRO GLU ALA GLY ASN TYR SEQRES 5 A 140 HIS ALA SER ILE HIS GLU LYS GLY ASP VAL SER LYS GLY SEQRES 6 A 140 VAL GLU SER THR GLY LYS VAL TRP HIS LYS PHE ASP GLU SEQRES 7 A 140 PRO ILE GLU CYS PHE ASN GLU SER ASP LEU GLY LYS ASN SEQRES 8 A 140 LEU TYR SER GLY LYS THR PHE LEU SER ALA PRO LEU PRO SEQRES 9 A 140 THR TRP GLN LEU ILE GLY ARG SER PHE VAL ILE SER LYS SEQRES 10 A 140 SER LEU ASN HIS PRO GLU ASN GLU PRO SER SER VAL LYS SEQRES 11 A 140 ASP TYR SER PHE LEU GLY VAL ILE ALA ARG HET CA A 218 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *112(H2 O) HELIX 1 1 LYS A 141 THR A 146 5 6 HELIX 2 2 PRO A 181 LEU A 185 5 5 HELIX 3 3 HIS A 198 GLU A 202 5 5 SHEET 1 A 5 SER A 79 GLU A 85 0 SHEET 2 A 5 VAL A 100 GLY A 110 -1 N ARG A 101 O LEU A 84 SHEET 3 A 5 LYS A 113 VAL A 123 -1 O LYS A 113 N VAL A 109 SHEET 4 A 5 LEU A 169 ALA A 178 -1 N TYR A 170 O VAL A 123 SHEET 5 A 5 ASN A 161 ASP A 164 -1 O ASN A 161 N SER A 171 SHEET 1 B 4 ASP A 208 VAL A 214 0 SHEET 2 B 4 SER A 189 SER A 195 -1 N PHE A 190 O GLY A 213 SHEET 3 B 4 GLY A 127 HIS A 134 -1 N HIS A 130 O SER A 193 SHEET 4 B 4 VAL A 149 LYS A 152 -1 N TRP A 150 O ILE A 133 SHEET 1 C 4 ASP A 208 VAL A 214 0 SHEET 2 C 4 SER A 189 SER A 195 -1 N PHE A 190 O GLY A 213 SHEET 3 C 4 GLY A 127 HIS A 134 -1 N HIS A 130 O SER A 193 SHEET 4 C 4 ILE A 157 CYS A 159 -1 N ILE A 157 O TYR A 129 LINK O PRO A 124 CA CA A 218 1555 1555 2.28 LINK O ASN A 168 CA CA A 218 1555 1555 2.60 LINK OD1 ASN A 168 CA CA A 218 1555 1555 2.45 LINK CA CA A 218 O HOH A1002 1555 1555 2.50 LINK CA CA A 218 O HOH A1003 1555 1555 2.28 LINK CA CA A 218 O HOH A1004 1555 4545 2.49 LINK CA CA A 218 O HOH A1005 1555 1555 2.44 CISPEP 1 PRO A 203 SER A 204 0 -5.13 SITE 1 AC1 6 PRO A 124 ASN A 168 HOH A1002 HOH A1003 SITE 2 AC1 6 HOH A1004 HOH A1005 CRYST1 34.154 46.326 73.907 90.00 90.00 90.00 P 21 21 21 4 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 0.029279 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013531 0.00000