10 20 30 40 50 60 70 80 1CC8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL TRANSPORT 04-MAR-99 1CC8
TITLE CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (METALLOCHAPERONE ATX1); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11D; SOURCE 9 EXPRESSION_SYSTEM_GENE: ATX1
KEYWDS COPPER TRANSPORT, MERCURY COORDINATION, METAL TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR A.C.ROSENZWEIG,D.L.HUFFMAN,M.Y.R.A.PUFAHL,T.V.O.HOU, AUTHOR 2 A.K.WERNIMONT
REVDAT 3 24-FEB-09 1CC8 1 VERSN REVDAT 2 01-APR-03 1CC8 1 JRNL REVDAT 1 12-DEC-99 1CC8 0
JRNL AUTH A.C.ROSENZWEIG,D.L.HUFFMAN,M.Y.HOU,A.K.WERNIMONT, JRNL AUTH 2 R.A.PUFAHL,T.V.O'HALLORAN JRNL TITL CRYSTAL STRUCTURE OF THE ATX1 METALLOCHAPERONE JRNL TITL 2 PROTEIN AT 1.02 A RESOLUTION. JRNL REF STRUCTURE FOLD.DES. V. 7 605 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10404590 JRNL DOI 10.1016/S0969-2126(99)80082-3
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.02 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.141 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.146 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2812 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25378 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.139 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.145 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2812 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 25378 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 567 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 701.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 596.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5745 REMARK 3 NUMBER OF RESTRAINTS : 6701 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.052 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.130 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.108 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.055 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.039 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1CC8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-99. REMARK 100 THE RCSB ID CODE IS RCSB000585.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0047 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24099 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.10600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SHAKE-N-BAKE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.32500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.80000 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 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 MET A 1
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 GLY A 64 O - C - N ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 68 CD - NE - CZ ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES 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 HG A 74 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 CYS A 15 SG 102.3 REMARK 620 3 CYS A 15 N 61.9 74.8 REMARK 620 4 CYS A 15 O 106.0 75.3 45.8 REMARK 620 5 CYS A 18 SG 83.6 167.3 98.8 92.3 REMARK 620 6 CYS A 18 N 146.1 97.6 98.2 53.4 72.2 REMARK 620 7 HOH A1018 O 136.7 84.9 156.0 117.1 98.6 71.7 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 HG A 74 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 186 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 187
DBREF 1CC8 A 1 73 UNP P38636 ATX1_YEAST 1 73
SEQRES 1 A 73 MET ALA GLU ILE LYS HIS TYR GLN PHE ASN VAL VAL MET SEQRES 2 A 73 THR CYS SER GLY CYS SER GLY ALA VAL ASN LYS VAL LEU SEQRES 3 A 73 THR LYS LEU GLU PRO ASP VAL SER LYS ILE ASP ILE SER SEQRES 4 A 73 LEU GLU LYS GLN LEU VAL ASP VAL TYR THR THR LEU PRO SEQRES 5 A 73 TYR ASP PHE ILE LEU GLU LYS ILE LYS LYS THR GLY LYS SEQRES 6 A 73 GLU VAL ARG SER GLY LYS GLN LEU
HET HG A 74 1 HET BEN A 186 9 HET BEN A 187 9
HETNAM HG MERCURY (II) ION HETNAM BEN BENZAMIDINE
FORMUL 2 HG HG 2+ FORMUL 3 BEN 2(C7 H8 N2) FORMUL 5 HOH *117(H2 O)
HELIX 1 1 SER A 16 LEU A 29 1 14 HELIX 2 2 TYR A 53 THR A 63 1 11
SHEET 1 A 4 VAL A 67 LEU A 73 0 SHEET 2 A 4 LYS A 5 VAL A 11 -1 N ASN A 10 O ARG A 68 SHEET 3 A 4 LEU A 44 THR A 49 -1 N THR A 49 O LYS A 5 SHEET 4 A 4 VAL A 33 SER A 39 -1 N SER A 39 O LEU A 44
LINK HG HG A 74 OG1 THR A 14 1555 1555 3.08 LINK HG HG A 74 SG CYS A 15 1555 1555 2.33 LINK HG HG A 74 N CYS A 15 1555 1555 3.26 LINK HG HG A 74 O CYS A 15 1555 1555 3.46 LINK HG HG A 74 SG CYS A 18 1555 1555 2.34 LINK HG HG A 74 N CYS A 18 1555 1555 3.14 LINK HG HG A 74 O HOH A1018 1555 1545 3.12
CISPEP 1 GLU A 30 PRO A 31 0 7.72
SITE 1 AC1 3 THR A 14 CYS A 15 CYS A 18 SITE 1 AC2 8 ILE A 4 ASN A 23 GLU A 30 VAL A 33 SITE 2 AC2 8 SER A 34 ILE A 36 LEU A 73 HOH A1002 SITE 1 AC3 7 MET A 13 LEU A 40 GLN A 43 GLU A 58 SITE 2 AC3 7 HOH A1039 HOH A1100 HOH A1109
CRYST1 56.650 29.600 40.770 90.00 114.83 90.00 C 1 2 1 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 0.017652 0.000000 0.008168 0.00000
SCALE2 0.000000 0.033784 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027026 0.00000