10 20 30 40 50 60 70 80 1CKU - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSFER PROTEIN 24-APR-99 1CKU
TITLE AB INITIO SOLUTION AND REFINEMENT OF TWO HIGH POTENTIAL TITLE 2 IRON PROTEIN STRUCTURES AT ATOMIC RESOLUTION
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HIPIP); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALLOCHROMATIUM VINOSUM; SOURCE 3 ORGANISM_TAXID: 1049; SOURCE 4 STRAIN: XL1BLUE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1BLUE; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLEHP20
KEYWDS ELECTRON TRANSFER PROTEIN, ATOMIC RESOLUTION, DIRECT KEYWDS 2 METHODS, IRON-SULPHUR CLUSTER, METALLOPROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR E.PARISINI,F.CAPOZZI,P.LUBINI,V.LAMZIN,C.LUCHINAT, AUTHOR 2 G.M.SHELDRICK
REVDAT 4 24-FEB-09 1CKU 1 VERSN REVDAT 3 01-APR-03 1CKU 1 JRNL REVDAT 2 24-NOV-99 1CKU 1 JRNL REMARK REVDAT 1 13-MAY-99 1CKU 0
JRNL AUTH E.PARISINI,F.CAPOZZI,P.LUBINI,V.LAMZIN,C.LUCHINAT, JRNL AUTH 2 G.M.SHELDRICK JRNL TITL AB INITIO SOLUTION AND REFINEMENT OF TWO JRNL TITL 2 HIGH-POTENTIAL IRON PROTEIN STRUCTURES AT ATOMIC JRNL TITL 3 RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1773 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10531472 JRNL DOI 10.1107/S0907444999009129
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.W.CARTER,J.KRAUT,S.T.FREER,N.-H.XUONG,R.A.ALDEN, REMARK 1 AUTH 2 R.G.BARTSCH REMARK 1 TITL TWO-ANGSTROM CRYSTAL STRUCTURE OF OXIDIZED REMARK 1 TITL 2 CHROMATIUM HIGH POTENTIAL IRON PROTEIN REMARK 1 REF J.BIOL.CHEM. V. 249 4212 1974 REMARK 1 REFN ISSN 0021-9258
REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.132 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1321 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 51872 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.124 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1220 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 47329 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1249 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1562.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1182.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14394 REMARK 3 NUMBER OF RESTRAINTS : 17533 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.126 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.070 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.076 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.057 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.031 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.083 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: NO RESTRAINTS ON PROSTHETIC GROUPS (RESIDUE 87 REMARK 3 IN CHAINS A AND B) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) BY ?
REMARK 4 REMARK 4 1CKU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-99. REMARK 100 THE RCSB ID CODE IS RCSB000936.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9091 REMARK 200 MONOCHROMATOR : GE SINGLE CRYSTAL REMARK 200 OPTICS : BENT CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 50551 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 12.500 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M AMMONIUM SULPHATE, 40 MM TRIS REMARK 280 180 MM KCL, PH 5.3
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 17.53350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.69450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.53350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.69450 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 33 NH1 - CZ - NH2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -8.6 DEGREES REMARK 500 LYS B 18 CG - CD - CE ANGL. DEV. = 23.4 DEGREES REMARK 500 ARG B 33 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ALA B 84 CA - C - N ANGL. DEV. = 13.6 DEGREES REMARK 500 ALA B 84 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 87 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 B 87
DBREF 1CKU A 1 85 UNP P00260 HIP_CHRVI 38 122 DBREF 1CKU B 1 85 UNP P00260 HIP_CHRVI 38 122
SEQRES 1 A 85 SER ALA PRO ALA ASN ALA VAL ALA ALA ASP ASP ALA THR SEQRES 2 A 85 ALA ILE ALA LEU LYS TYR ASN GLN ASP ALA THR LYS SER SEQRES 3 A 85 GLU ARG VAL ALA ALA ALA ARG PRO GLY LEU PRO PRO GLU SEQRES 4 A 85 GLU GLN HIS CYS ALA ASN CYS GLN PHE MET GLN ALA ASP SEQRES 5 A 85 ALA ALA GLY ALA THR ASP GLU TRP LYS GLY CYS GLN LEU SEQRES 6 A 85 PHE PRO GLY LYS LEU ILE ASN VAL ASN GLY TRP CYS ALA SEQRES 7 A 85 SER TRP THR LEU LYS ALA GLY SEQRES 1 B 85 SER ALA PRO ALA ASN ALA VAL ALA ALA ASP ASP ALA THR SEQRES 2 B 85 ALA ILE ALA LEU LYS TYR ASN GLN ASP ALA THR LYS SER SEQRES 3 B 85 GLU ARG VAL ALA ALA ALA ARG PRO GLY LEU PRO PRO GLU SEQRES 4 B 85 GLU GLN HIS CYS ALA ASN CYS GLN PHE MET GLN ALA ASP SEQRES 5 B 85 ALA ALA GLY ALA THR ASP GLU TRP LYS GLY CYS GLN LEU SEQRES 6 B 85 PHE PRO GLY LYS LEU ILE ASN VAL ASN GLY TRP CYS ALA SEQRES 7 B 85 SER TRP THR LEU LYS ALA GLY
HET SF4 A 87 8 HET SF4 B 87 8
HETNAM SF4 IRON/SULFUR CLUSTER
FORMUL 3 SF4 2(FE4 S4) FORMUL 5 HOH *334(H2 O)
HELIX 1 1 ALA A 12 LEU A 17 1 6 HELIX 2 2 ALA A 23 LYS A 25 5 3 HELIX 3 3 ARG A 28 ALA A 31 1 4 HELIX 4 4 PRO A 38 GLU A 40 5 3 HELIX 5 5 CYS A 43 ASN A 45 5 3 HELIX 6 6 ALA B 12 LEU B 17 1 6 HELIX 7 7 ALA B 23 LYS B 25 5 3 HELIX 8 8 ARG B 28 ALA B 31 1 4 HELIX 9 9 PRO B 38 GLU B 40 5 3 HELIX 10 10 CYS B 43 ASN B 45 5 3
SHEET 1 A 2 TRP A 60 GLY A 62 0 SHEET 2 A 2 LEU A 70 ASN A 72 -1 N ILE A 71 O LYS A 61
LINK FE1 SF4 A 87 SG CYS A 43 1555 1555 2.25 LINK FE2 SF4 A 87 SG CYS A 46 1555 1555 2.30 LINK FE3 SF4 A 87 SG CYS A 63 1555 1555 2.27 LINK FE4 SF4 A 87 SG CYS A 77 1555 1555 2.28 LINK FE1 SF4 B 87 SG CYS B 43 1555 1555 2.27 LINK FE2 SF4 B 87 SG CYS B 46 1555 1555 2.30 LINK FE3 SF4 B 87 SG CYS B 63 1555 1555 2.27 LINK FE4 SF4 B 87 SG CYS B 77 1555 1555 2.27
SITE 1 AC1 6 TYR A 19 CYS A 43 CYS A 46 PHE A 48 SITE 2 AC1 6 CYS A 63 CYS A 77 SITE 1 AC2 6 CYS B 43 CYS B 46 PHE B 48 CYS B 63 SITE 2 AC2 6 LEU B 65 CYS B 77
CRYST1 35.067 51.389 92.390 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 0.028517 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019459 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010824 0.00000
MTRIX1 1 -0.752710 0.641490 -0.148050 12.33340 1
MTRIX2 1 0.656950 0.717180 -0.232530 -7.05840 1
MTRIX3 1 -0.042980 -0.272290 -0.961250 34.58648 1