HEADER ELECTRON TRANSPORT 27-OCT-17 5YOC TITLE CRYSTAL STRUCTURE OF FLAVODOXIN WITH ENGINEERED DISULFIDE BOND C102- TITLE 2 R125C COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVODOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH / SOURCE 3 ATCC 29579 / DSM 644 / NCIMB 8303); SOURCE 4 ORGANISM_TAXID: 882; SOURCE 5 STRAIN: HILDENBOROUGH / ATCC 29579 / DSM 644 / NCIMB 8303; SOURCE 6 GENE: DVU_2680; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FUSION PARTNER, FMN BINDING PROTEIN, OXIDATION., ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.PU,Z.XU,G.SONG,Z.J.LIU REVDAT 3 22-NOV-23 5YOC 1 REMARK REVDAT 2 11-JUL-18 5YOC 1 JRNL REVDAT 1 27-DEC-17 5YOC 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 22920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1402 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 40.6435 - 3.2313 0.95 2126 137 0.1521 0.1652 REMARK 3 2 3.2313 - 2.5649 0.96 2130 139 0.1766 0.1849 REMARK 3 3 2.5649 - 2.2407 0.98 2147 138 0.1758 0.1944 REMARK 3 4 2.2407 - 2.0358 0.99 2137 143 0.1694 0.1840 REMARK 3 5 2.0358 - 1.8899 0.99 2150 137 0.1624 0.2057 REMARK 3 6 1.8899 - 1.7785 0.99 2182 142 0.1720 0.1962 REMARK 3 7 1.7785 - 1.6894 0.99 2168 140 0.1802 0.2149 REMARK 3 8 1.6894 - 1.6159 1.00 2140 145 0.1874 0.2323 REMARK 3 9 1.6159 - 1.5537 1.00 2193 137 0.2054 0.2296 REMARK 3 10 1.5537 - 1.5000 0.99 2145 144 0.2229 0.2686 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 1194 REMARK 3 ANGLE : 0.821 1632 REMARK 3 CHIRALITY : 0.052 177 REMARK 3 PLANARITY : 0.004 214 REMARK 3 DIHEDRAL : 15.832 684 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 5YOC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.5 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 : 22931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.629 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7600 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: 1J8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL 0.1M AMMONIUM SULFA 3.1M, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.03650 REMARK 290 SMTRY3 2 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 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 499 O HOH A 516 1.87 REMARK 500 O HOH A 348 O HOH A 477 1.91 REMARK 500 O HOH A 348 O HOH A 349 1.94 REMARK 500 O HOH A 380 O HOH A 490 1.96 REMARK 500 O HOH A 386 O HOH A 533 2.01 REMARK 500 OD1 ASP A 34 O HOH A 301 2.07 REMARK 500 O HOH A 443 O HOH A 512 2.07 REMARK 500 NH1 ARG A 134 O HOH A 302 2.07 REMARK 500 OE1 GLU A 79 O HOH A 303 2.08 REMARK 500 NE2 GLN A 84 O HOH A 304 2.09 REMARK 500 OD1 ASP A 106 O HOH A 305 2.12 REMARK 500 O HOH A 345 O HOH A 353 2.12 REMARK 500 O3 GOL A 202 O HOH A 306 2.13 REMARK 500 NH2 ARG A 134 O HOH A 307 2.13 REMARK 500 OE2 GLU A 99 O HOH A 308 2.16 REMARK 500 O HOH A 468 O HOH A 483 2.16 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 302 O HOH A 350 28510 1.87 REMARK 500 O HOH A 317 O HOH A 509 28510 2.04 REMARK 500 O HOH A 430 O HOH A 437 2849 2.04 REMARK 500 O HOH A 310 O HOH A 474 2849 2.19 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 ASP A 63 31.57 -146.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 559 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 560 DISTANCE = 6.59 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5YOB RELATED DB: PDB REMARK 900 RELATED ID: 5YOG RELATED DB: PDB REMARK 900 RELATED ID: 5YOE RELATED DB: PDB DBREF 5YOC A 3 148 UNP P00323 FLAV_DESVH 3 148 SEQADV 5YOC SER A 1 UNP P00323 EXPRESSION TAG SEQADV 5YOC ALA A 2 UNP P00323 EXPRESSION TAG SEQADV 5YOC TRP A 98 UNP P00323 TYR 98 ENGINEERED MUTATION SEQADV 5YOC CYS A 125 UNP P00323 ARG 125 ENGINEERED MUTATION SEQRES 1 A 148 SER ALA LYS ALA LEU ILE VAL TYR GLY SER THR THR GLY SEQRES 2 A 148 ASN THR GLU TYR THR ALA GLU THR ILE ALA ARG GLU LEU SEQRES 3 A 148 ALA ASP ALA GLY TYR GLU VAL ASP SER ARG ASP ALA ALA SEQRES 4 A 148 SER VAL GLU ALA GLY GLY LEU PHE GLU GLY PHE ASP LEU SEQRES 5 A 148 VAL LEU LEU GLY CYS SER THR TRP GLY ASP ASP SER ILE SEQRES 6 A 148 GLU LEU GLN ASP ASP PHE ILE PRO LEU PHE ASP SER LEU SEQRES 7 A 148 GLU GLU THR GLY ALA GLN GLY ARG LYS VAL ALA CYS PHE SEQRES 8 A 148 GLY CYS GLY ASP SER SER TRP GLU TYR PHE CYS GLY ALA SEQRES 9 A 148 VAL ASP ALA ILE GLU GLU LYS LEU LYS ASN LEU GLY ALA SEQRES 10 A 148 GLU ILE VAL GLN ASP GLY LEU CYS ILE ASP GLY ASP PRO SEQRES 11 A 148 ARG ALA ALA ARG ASP ASP ILE VAL GLY TRP ALA HIS ASP SEQRES 12 A 148 VAL ARG GLY ALA ILE HET FMN A 201 50 HET GOL A 202 14 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM GOL GLYCEROL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *260(H2 O) HELIX 1 AA1 GLY A 13 GLY A 30 1 18 HELIX 2 AA2 ALA A 39 VAL A 41 5 3 HELIX 3 AA3 PHE A 71 SER A 77 1 7 HELIX 4 AA4 LEU A 78 THR A 81 5 4 HELIX 5 AA5 CYS A 102 LEU A 115 1 14 HELIX 6 AA6 ASP A 129 ALA A 132 5 4 HELIX 7 AA7 ALA A 133 ALA A 147 1 15 SHEET 1 AA1 5 GLU A 32 ASP A 37 0 SHEET 2 AA1 5 LYS A 3 GLY A 9 1 N ILE A 6 O ARG A 36 SHEET 3 AA1 5 LEU A 52 CYS A 57 1 O LEU A 54 N LEU A 5 SHEET 4 AA1 5 LYS A 87 GLY A 94 1 O PHE A 91 N LEU A 55 SHEET 5 AA1 5 GLU A 118 ILE A 119 1 O GLU A 118 N VAL A 88 SHEET 1 AA2 5 GLU A 32 ASP A 37 0 SHEET 2 AA2 5 LYS A 3 GLY A 9 1 N ILE A 6 O ARG A 36 SHEET 3 AA2 5 LEU A 52 CYS A 57 1 O LEU A 54 N LEU A 5 SHEET 4 AA2 5 LYS A 87 GLY A 94 1 O PHE A 91 N LEU A 55 SHEET 5 AA2 5 LEU A 124 ASP A 127 1 O ILE A 126 N GLY A 94 SHEET 1 AA3 2 THR A 59 TRP A 60 0 SHEET 2 AA3 2 GLU A 66 LEU A 67 -1 O GLU A 66 N TRP A 60 SSBOND 1 CYS A 102 CYS A 125 1555 1555 2.02 SITE 1 AC1 23 SER A 10 THR A 11 THR A 12 GLY A 13 SITE 2 AC1 23 ASN A 14 THR A 15 SER A 58 THR A 59 SITE 3 AC1 23 TRP A 60 GLY A 61 CYS A 93 GLY A 94 SITE 4 AC1 23 ASP A 95 TRP A 98 TYR A 100 PHE A 101 SITE 5 AC1 23 CYS A 102 HOH A 355 HOH A 415 HOH A 437 SITE 6 AC1 23 HOH A 442 HOH A 450 HOH A 467 SITE 1 AC2 1 HOH A 306 CRYST1 32.300 56.073 41.328 90.00 100.56 90.00 P 1 21 1 2 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 0.030960 0.000000 0.005769 0.00000 SCALE2 0.000000 0.017834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024613 0.00000