HEADER ELECTRON TRANSPORT 18-SEP-96 1HCZ TITLE LUMEN-SIDE DOMAIN OF REDUCED CYTOCHROME F AT-35 DEGREES CELSIUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME F; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRASSICA RAPA; SOURCE 3 ORGANISM_TAXID: 3711; SOURCE 4 ORGAN: LEAF; SOURCE 5 ORGANELLE: CHLOROPLAST KEYWDS ELECTRON TRANSPORT, PHOTOSYNTHESIS, CYTOCHROME B6F COMPLEX, KEYWDS 2 CHLOROPLAST TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.MARTINEZ,D.HUANG,A.SZCZEPANIAK,W.A.CRAMER,J.L.SMITH REVDAT 4 30-OCT-24 1HCZ 1 REMARK REVDAT 3 05-JUN-24 1HCZ 1 REMARK LINK REVDAT 2 24-FEB-09 1HCZ 1 VERSN REVDAT 1 12-MAR-97 1HCZ 0 JRNL AUTH S.E.MARTINEZ,D.HUANG,M.PONOMAREV,W.A.CRAMER,J.L.SMITH JRNL TITL THE HEME REDOX CENTER OF CHLOROPLAST CYTOCHROME F IS LINKED JRNL TITL 2 TO A BURIED FIVE-WATER CHAIN. JRNL REF PROTEIN SCI. V. 5 1081 1996 JRNL REFN ISSN 0961-8368 JRNL PMID 8762139 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.E.MARTINEZ,D.HUANG,A.SZCZEPANIAK,W.A.CRAMER,J.L.SMITH REMARK 1 TITL CRYSTAL STRUCTURE OF CHLOROPLAST CYTOCHROME F REVEALS A REMARK 1 TITL 2 NOVEL CYTOCHROME FOLD AND UNEXPECTED HEME LIGATION REMARK 1 REF STRUCTURE V. 2 95 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5A REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 19639 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 986 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.013 ; 8.000 ; 2018 REMARK 3 BOND ANGLES (DEGREES) : 1.500 ; 10.000; 2754 REMARK 3 TORSION ANGLES (DEGREES) : 20.600; 20.000; 1319 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : 19.900; 20.000; 22 REMARK 3 TRIGONAL CARBON PLANES (A) : 0.017 ; 9.000 ; 59 REMARK 3 GENERAL PLANES (A) : 0.017 ; 30.000; 282 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.600 ; 0.400 ; 1826 REMARK 3 NON-BONDED CONTACTS (A) : 0.048 ; 20.000; 64 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : TNT BULK SOLVENT CORRECTION REMARK 3 KSOL : 0.73 REMARK 3 BSOL : 251.3 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1992 REMARK 200 TEMPERATURE (KELVIN) : 238 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21059 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 39.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.10000 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 VAL A 251 REMARK 465 GLN A 252 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 ASN A 99 22.36 -69.40 REMARK 500 ASN A 168 47.72 -96.72 REMARK 500 ASP A 224 -7.36 76.33 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 HEM A 253 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 1 N REMARK 620 2 HEM A 253 NA 87.0 REMARK 620 3 HEM A 253 NB 91.8 91.6 REMARK 620 4 HEM A 253 NC 91.4 178.4 88.2 REMARK 620 5 HEM A 253 ND 86.2 89.5 177.7 90.6 REMARK 620 6 HIS A 25 NE2 176.4 91.1 91.3 90.5 90.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 253 DBREF 1HCZ A 1 252 UNP P36438 CYF_BRARA 36 287 SEQRES 1 A 252 TYR PRO ILE PHE ALA GLN GLN ASN TYR GLU ASN PRO ARG SEQRES 2 A 252 GLU ALA THR GLY ARG ILE VAL CYS ALA ASN CYS HIS LEU SEQRES 3 A 252 ALA SER LYS PRO VAL ASP ILE GLU VAL PRO GLN ALA VAL SEQRES 4 A 252 LEU PRO ASP THR VAL PHE GLU ALA VAL VAL LYS ILE PRO SEQRES 5 A 252 TYR ASP MET GLN LEU LYS GLN VAL LEU ALA ASN GLY LYS SEQRES 6 A 252 LYS GLY ALA LEU ASN VAL GLY ALA VAL LEU ILE LEU PRO SEQRES 7 A 252 GLU GLY PHE GLU LEU ALA PRO PRO ASP ARG ILE SER PRO SEQRES 8 A 252 GLU MET LYS GLU LYS ILE GLY ASN LEU SER PHE GLN ASN SEQRES 9 A 252 TYR ARG PRO ASN LYS LYS ASN ILE LEU VAL ILE GLY PRO SEQRES 10 A 252 VAL PRO GLY GLN LYS TYR SER GLU ILE THR PHE PRO ILE SEQRES 11 A 252 LEU ALA PRO ASP PRO ALA THR ASN LYS ASP VAL HIS PHE SEQRES 12 A 252 LEU LYS TYR PRO ILE TYR VAL GLY GLY ASN ARG GLY ARG SEQRES 13 A 252 GLY GLN ILE TYR PRO ASP GLY SER LYS SER ASN ASN THR SEQRES 14 A 252 VAL TYR ASN ALA THR ALA GLY GLY ILE ILE SER LYS ILE SEQRES 15 A 252 LEU ARG LYS GLU LYS GLY GLY TYR GLU ILE THR ILE VAL SEQRES 16 A 252 ASP ALA SER ASN GLU ARG GLN VAL ILE ASP ILE ILE PRO SEQRES 17 A 252 ARG GLY LEU GLU LEU LEU VAL SER GLU GLY GLU SER ILE SEQRES 18 A 252 LYS LEU ASP GLN PRO LEU THR SER ASN PRO ASN VAL GLY SEQRES 19 A 252 GLY PHE GLY GLN GLY ASP ALA GLU ILE VAL LEU GLN ASP SEQRES 20 A 252 PRO LEU ARG VAL GLN HET HEM A 253 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *408(H2 O) HELIX 1 1 PRO A 2 ASN A 8 1 7 HELIX 2 2 VAL A 20 ASN A 23 5 4 HELIX 3 3 PRO A 86 ARG A 88 5 3 HELIX 4 4 PRO A 91 ILE A 97 1 7 HELIX 5 5 GLY A 120 TYR A 123 1 4 SHEET 1 A 3 ASP A 32 GLU A 34 0 SHEET 2 A 3 VAL A 44 LYS A 50 -1 N LYS A 50 O ASP A 32 SHEET 3 A 3 GLU A 125 LEU A 131 -1 N ILE A 130 O PHE A 45 SHEET 1 B 5 ALA A 38 LEU A 40 0 SHEET 2 B 5 GLY A 235 GLN A 246 1 N VAL A 244 O VAL A 39 SHEET 3 B 5 LYS A 145 ARG A 154 -1 N ARG A 154 O GLY A 235 SHEET 4 B 5 VAL A 71 ILE A 76 -1 N ILE A 76 O TYR A 149 SHEET 5 B 5 ILE A 112 ILE A 115 -1 N ILE A 115 O ALA A 73 SHEET 1 C 3 ARG A 201 ILE A 207 0 SHEET 2 C 3 TYR A 190 ASP A 196 -1 N ASP A 196 O ARG A 201 SHEET 3 C 3 ILE A 178 ARG A 184 -1 N LEU A 183 O GLU A 191 LINK SG CYS A 21 CAB HEM A 253 1555 1555 1.79 LINK SG CYS A 24 CAC HEM A 253 1555 1555 1.79 LINK N TYR A 1 FE HEM A 253 1555 1555 1.94 LINK NE2 HIS A 25 FE HEM A 253 1555 1555 1.93 CISPEP 1 GLY A 116 PRO A 117 0 1.28 SITE 1 AC1 21 TYR A 1 PRO A 2 PHE A 4 ALA A 5 SITE 2 AC1 21 CYS A 21 CYS A 24 HIS A 25 GLN A 59 SITE 3 AC1 21 LEU A 69 ASN A 70 VAL A 71 GLY A 72 SITE 4 AC1 21 ASN A 153 GLY A 155 ARG A 156 GLY A 157 SITE 5 AC1 21 ILE A 159 TYR A 160 PRO A 161 HOH A 292 SITE 6 AC1 21 HOH A 363 CRYST1 78.600 82.200 45.200 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 0.012723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022124 0.00000