HEADER ELECTRON TRANSPORT 26-OCT-17 5YO6 TITLE CRYSTAL STRUCTURE OF B562RIL WITH ENGINEERED DISULFIDE BOND T9C-A36C COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: B562RIL, CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEMOPROTEIN, FUSION PARTNER, HELIX BUNDLE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.PU,Z.XU,G.SONG,Z.J.LIU REVDAT 3 22-NOV-23 5YO6 1 REMARK REVDAT 2 11-JUL-18 5YO6 1 JRNL REVDAT 1 14-MAR-18 5YO6 0 JRNL AUTH M.PU,Z.XU,Y.PENG,Y.HOU,D.LIU,Y.WANG,H.LIU,G.SONG,Z.J.LIU JRNL TITL PROTEIN CRYSTAL QUALITY ORIENTED DISULFIDE BOND ENGINEERING. JRNL REF PROTEIN CELL V. 9 659 2018 JRNL REFN ESSN 1674-8018 JRNL PMID 29039033 JRNL DOI 10.1007/S13238-017-0482-7 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.8 REMARK 3 NUMBER OF REFLECTIONS : 22726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 32.2829 - 2.9013 0.96 1998 193 0.2070 0.2157 REMARK 3 2 2.9013 - 2.3030 1.00 1985 192 0.2115 0.2567 REMARK 3 3 2.3030 - 2.0119 1.00 1980 190 0.1966 0.2239 REMARK 3 4 2.0119 - 1.8280 1.00 1926 185 0.2189 0.2693 REMARK 3 5 1.8280 - 1.6970 1.00 1976 191 0.2197 0.2279 REMARK 3 6 1.6970 - 1.5969 1.00 1939 187 0.2163 0.2527 REMARK 3 7 1.5969 - 1.5170 1.00 1931 187 0.2261 0.2203 REMARK 3 8 1.5170 - 1.4509 0.96 1858 179 0.2263 0.2437 REMARK 3 9 1.4509 - 1.3951 0.79 1536 147 0.2305 0.2708 REMARK 3 10 1.3951 - 1.3469 0.65 1240 120 0.2506 0.2454 REMARK 3 11 1.3469 - 1.3048 0.50 962 94 0.2427 0.3177 REMARK 3 12 1.3048 - 1.2675 0.39 744 71 0.2577 0.2602 REMARK 3 13 1.2675 - 1.2342 0.25 474 45 0.3130 0.3099 REMARK 3 14 1.2342 - 1.2040 0.09 178 18 0.3426 0.3574 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 850 REMARK 3 ANGLE : 0.850 1149 REMARK 3 CHIRALITY : 0.065 128 REMARK 3 PLANARITY : 0.007 153 REMARK 3 DIHEDRAL : 21.212 331 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 5YO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0-9.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22730 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.204 REMARK 200 RESOLUTION RANGE LOW (A) : 32.271 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.0 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.4900 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 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 REMARK 200 STARTING MODEL: 1M6T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M NH4(SO4), 0.1M BICINE 2.44MM N REMARK 280 -OCTANOYLSUCROSE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 44.84250 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 44.84250 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 20.88200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.42000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.88200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.42000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 44.84250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.88200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.42000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.84250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.88200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.42000 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: 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 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 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 428 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 402 O HOH A 426 1.88 REMARK 500 NH2 ARG A 62 O HOH A 301 1.98 REMARK 500 O HOH A 381 O HOH A 399 2.06 REMARK 500 O HOH A 380 O HOH A 402 2.08 REMARK 500 O HOH A 301 O HOH A 368 2.12 REMARK 500 O HOH A 394 O HOH A 403 2.16 REMARK 500 O HOH A 413 O HOH A 417 2.17 REMARK 500 O HOH A 318 O HOH A 388 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 355 O HOH A 392 4555 2.07 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 4 -58.86 96.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M6T RELATED DB: PDB DBREF 5YO6 A 1 106 UNP P0ABE7 C562_ECOLX 23 128 SEQADV 5YO6 TRP A 7 UNP P0ABE7 MET 29 ENGINEERED MUTATION SEQADV 5YO6 CYS A 9 UNP P0ABE7 THR 31 ENGINEERED MUTATION SEQADV 5YO6 CYS A 36 UNP P0ABE7 ALA 58 ENGINEERED MUTATION SEQADV 5YO6 ILE A 102 UNP P0ABE7 HIS 124 ENGINEERED MUTATION SEQADV 5YO6 LEU A 106 UNP P0ABE7 ARG 128 ENGINEERED MUTATION SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN TRP GLU CYS LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU THR LYS MET ARG ALA CYS ALA LEU ASP SEQRES 4 A 106 ALA GLN LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET LYS ASP PHE ARG HIS GLY PHE SEQRES 6 A 106 ASP ILE LEU VAL GLY GLN ILE ASP ASP ALA LEU LYS LEU SEQRES 7 A 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS THR THR ARG ASN ALA TYR ILE GLN LYS SEQRES 9 A 106 TYR LEU FORMUL 2 HOH *129(H2 O) HELIX 1 AA1 GLU A 4 ALA A 20 1 17 HELIX 2 AA2 ASN A 22 LYS A 42 1 21 HELIX 3 AA3 SER A 55 GLU A 81 1 27 HELIX 4 AA4 LYS A 83 ILE A 102 1 20 HELIX 5 AA5 GLN A 103 LEU A 106 5 4 SSBOND 1 CYS A 9 CYS A 36 1555 1555 2.03 CRYST1 41.764 50.840 89.685 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 0.023944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011150 0.00000