HEADER ELECTRON TRANSPORT 07-MAR-21 7EAD TITLE CRYSTAL STRUCTURE OF BETA-SHEET CYTOCHROME C PRIME FROM THERMUS TITLE 2 THERMOPHILUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME_P460 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: TTHHC11_22770; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOCHROME C, THERMOPHILE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.YOSHIMI,S.FUJII,H.OKI,T.IGAWA,R.H.ADAMS,K.UEDA,K.KAWAHARA,T.OHKUBO, AUTHOR 2 A.M.HOUGH,Y.SAMBONGI REVDAT 3 29-NOV-23 7EAD 1 REMARK REVDAT 2 15-JUN-22 7EAD 1 JRNL REVDAT 1 09-MAR-22 7EAD 0 JRNL AUTH T.YOSHIMI,S.FUJII,H.OKI,T.IGAWA,H.R.ADAMS,K.UEDA,K.KAWAHARA, JRNL AUTH 2 T.OHKUBO,M.A.HOUGH,Y.SAMBONGI JRNL TITL CRYSTAL STRUCTURE OF THERMALLY STABLE HOMODIMERIC CYTOCHROME JRNL TITL 2 C'-BETA FROM THERMUS THERMOPHILUS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 78 217 2022 JRNL REFN ESSN 2053-230X JRNL PMID 35647678 JRNL DOI 10.1107/S2053230X22005088 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.4200 - 3.7500 1.00 1306 150 0.1467 0.1646 REMARK 3 2 3.7500 - 2.9800 1.00 1252 152 0.1677 0.1509 REMARK 3 3 2.9700 - 2.6000 1.00 1258 123 0.1829 0.2106 REMARK 3 4 2.6000 - 2.3600 1.00 1231 136 0.2046 0.2060 REMARK 3 5 2.3600 - 2.1900 1.00 1223 142 0.1906 0.2384 REMARK 3 6 2.1900 - 2.0600 1.00 1222 136 0.2115 0.2696 REMARK 3 7 2.0600 - 1.9600 0.99 1196 141 0.2177 0.2613 REMARK 3 8 1.9600 - 1.8700 1.00 1212 137 0.2198 0.3043 REMARK 3 9 1.8700 - 1.8000 0.99 1218 134 0.2568 0.3157 REMARK 3 10 1.8000 - 1.7400 0.99 1199 131 0.2895 0.3846 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7EAD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021066. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 41.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.19700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.60 REMARK 200 R MERGE FOR SHELL (I) : 1.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.1 REMARK 200 STARTING MODEL: 6HIH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M 4-(2-HYDROXYETHYL)-1 REMARK 280 -PIPERAZINEETHANESULFONIC ACID BUFFER (PH 7.5) AND 20% (W/V) REMARK 280 POLYETHYLENE GLYCOL 10,000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 41.15250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.15250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.41500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.61250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.41500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.61250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.15250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.41500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.61250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.15250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.41500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.61250 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 365 LIES ON A SPECIAL POSITION. 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 HEC A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HEC A 201 NA 93.0 REMARK 620 3 HEC A 201 NB 93.8 89.2 REMARK 620 4 HEC A 201 NC 99.1 168.0 90.3 REMARK 620 5 HEC A 201 ND 95.0 89.1 171.2 89.6 REMARK 620 N 1 2 3 4 DBREF1 7EAD A 1 135 UNP A0A510IM14_THETH DBREF2 7EAD A A0A510IM14 20 154 SEQRES 1 A 135 GLY LEU PRO TYR PRO GLU GLY TYR ARG PHE TRP THR HIS SEQRES 2 A 135 VAL LYS SER MET GLU LEU LYS PRO GLY HIS PRO LEU TYR SEQRES 3 A 135 GLU SER PHE GLY GLY LEU HIS HIS ILE TYR VAL ASN PRO SEQRES 4 A 135 THR GLY LEU ARG THR TYR LEU GLU GLY LYS LYS ALA PRO SEQRES 5 A 135 PHE PRO LYS GLY THR VAL ILE VAL PHE ASP LEU LEU GLU SEQRES 6 A 135 ALA LYS VAL GLU GLY ASN ALA LEU LEU GLU GLY PRO ARG SEQRES 7 A 135 LYS LEU ILE GLY VAL MET ALA LYS ASP PRO GLY ARG TYR SEQRES 8 A 135 PRO ASP THR GLY GLY TRP GLY TYR TYR ALA PHE GLY PRO SEQRES 9 A 135 ASP LYS LYS PRO LEU ALA ILE ASP PRO LYS ALA CYS HIS SEQRES 10 A 135 ALA CYS HIS GLN GLY ALA ALA ASN THR ASP TYR VAL PHE SEQRES 11 A 135 SER ALA PHE ARG PRO HET HEC A 201 43 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 HOH *126(H2 O) HELIX 1 AA1 GLY A 7 TRP A 11 5 5 HELIX 2 AA2 LEU A 25 GLY A 30 1 6 HELIX 3 AA3 ASN A 38 GLU A 47 1 10 HELIX 4 AA4 TYR A 91 GLY A 95 5 5 HELIX 5 AA5 ASP A 112 GLN A 121 1 10 HELIX 6 AA6 GLY A 122 ASP A 127 5 6 SHEET 1 AA1 5 THR A 12 LEU A 19 0 SHEET 2 AA1 5 GLY A 31 VAL A 37 -1 O ILE A 35 N VAL A 14 SHEET 3 AA1 5 VAL A 58 VAL A 68 -1 O LEU A 64 N LEU A 32 SHEET 4 AA1 5 LEU A 73 LYS A 86 -1 O LEU A 74 N LYS A 67 SHEET 5 AA1 5 TRP A 97 PHE A 102 -1 O GLY A 98 N ALA A 85 LINK SG CYS A 116 CAB HEC A 201 1555 1555 1.77 LINK SG CYS A 119 CAC HEC A 201 1555 1555 1.78 LINK NE2 HIS A 120 FE HEC A 201 1555 1555 2.19 CRYST1 38.830 81.225 82.305 90.00 90.00 90.00 C 2 2 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 0.025753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012311 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012150 0.00000