HEADER ELECTRON TRANSPORT 06-SEP-19 6U97 TITLE STRUCTURE OF OMCF_H47I MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOPROTEIN CYTOCHROME C, 1 HEME-BINDING SITE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER SULFURREDUCENS (STRAIN ATCC 51573 / SOURCE 3 DSM 12127 / PCA); SOURCE 4 ORGANISM_TAXID: 243231; SOURCE 5 STRAIN: ATCC 51573 / DSM 12127 / PCA; SOURCE 6 GENE: OMCF, GSU2432; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OMCF, REDOX-BOHR EFFECT, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR P.R.POKKULURI REVDAT 1 19-FEB-20 6U97 0 JRNL AUTH L.R.TEIXEIRA,C.M.CORDAS,M.P.FONSECA,N.E.C.DUKE, JRNL AUTH 2 P.R.POKKULURI,C.A.SALGUEIRO JRNL TITL MODULATION OF THE REDOX POTENTIAL AND ELECTRON/PROTON JRNL TITL 2 TRANSFER MECHANISMS IN THE OUTER MEMBRANE CYTOCHROME OMCF JRNL TITL 3 FROMGEOBACTER SULFURREDUCENS. JRNL REF FRONT MICROBIOL V. 10 2941 2019 JRNL REFN ESSN 1664-302X JRNL PMID 32010071 JRNL DOI 10.3389/FMICB.2019.02941 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 64.7 REMARK 3 NUMBER OF REFLECTIONS : 18212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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 23.8700 - 2.0500 0.99 4626 229 0.1421 0.1710 REMARK 3 2 2.0500 - 1.6300 0.96 4269 235 0.1200 0.1310 REMARK 3 3 1.6300 - 1.4200 0.83 3691 185 0.0875 0.1242 REMARK 3 4 1.4200 - 1.2900 0.63 2789 146 0.0868 0.1331 REMARK 3 5 1.2900 - 1.2000 0.31 1385 73 0.0925 0.1362 REMARK 3 6 1.2000 - 1.1300 0.13 555 29 0.1672 0.2189 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) : 0.061 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.97 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 : 0.014 665 REMARK 3 ANGLE : 1.275 925 REMARK 3 CHIRALITY : 0.088 92 REMARK 3 PLANARITY : 0.012 120 REMARK 3 DIHEDRAL : 15.513 354 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 6U97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1000244203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-18 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31673 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NEEDLE CLUSTERS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES PH REMARK 280 7.5, 2% (V/V) PEG400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 19.09300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.60900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.50950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.60900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.09300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.50950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 29 CD OE1 OE2 REMARK 470 GLU A 49 CD OE1 OE2 REMARK 470 ARG A 63 CD NE CZ NH1 NH2 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 SG CYS A 35 HAB HEM A 202 1.51 REMARK 500 HH12 ARG A 57 O HOH A 301 1.60 REMARK 500 O HOH A 307 O HOH A 317 1.86 REMARK 500 O HOH A 353 O HOH A 362 2.12 REMARK 500 O HOH A 372 O HOH A 375 2.16 REMARK 500 O HOH A 328 O HOH A 376 2.18 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 ASN A 74 72.64 -152.71 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 392 DISTANCE = 5.85 ANGSTROMS 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 202 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEM A 202 NA 89.7 REMARK 620 3 HEM A 202 NB 89.0 91.4 REMARK 620 4 HEM A 202 NC 89.7 179.4 88.8 REMARK 620 5 HEM A 202 ND 90.5 88.5 179.5 91.3 REMARK 620 6 MET A 79 SD 177.4 87.8 91.7 92.8 88.8 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 202 DBREF 6U97 A 24 104 UNP Q74AE4 Q74AE4_GEOSL 24 104 SEQADV 6U97 ALA A 23 UNP Q74AE4 EXPRESSION TAG SEQADV 6U97 ILE A 47 UNP Q74AE4 HIS 47 ENGINEERED MUTATION SEQRES 1 A 82 ALA GLY ALA GLY GLY GLY GLU LEU PHE ALA THR HIS CYS SEQRES 2 A 82 ALA GLY CYS HIS PRO GLN GLY GLY ASN THR VAL ILE PRO SEQRES 3 A 82 GLU LYS THR LEU ALA ARG ALA ARG ARG GLU ALA ASN GLY SEQRES 4 A 82 ILE ARG THR VAL ARG ASP VAL ALA ALA TYR ILE ARG ASN SEQRES 5 A 82 PRO GLY PRO GLY MET PRO ALA PHE GLY GLU ALA MET ILE SEQRES 6 A 82 PRO PRO ALA ASP ALA LEU LYS ILE GLY GLU TYR VAL VAL SEQRES 7 A 82 ALA SER PHE PRO HET SO4 A 201 5 HET HEM A 202 73 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *92(H2 O) HELIX 1 AA1 GLY A 26 CYS A 35 1 10 HELIX 2 AA2 HIS A 39 GLY A 43 5 5 HELIX 3 AA3 ALA A 53 ASN A 60 1 8 HELIX 4 AA4 THR A 64 ILE A 72 1 9 HELIX 5 AA5 PRO A 88 PHE A 103 1 16 LINK SG CYS A 35 CAB HEM A 202 1555 1555 1.87 LINK SG CYS A 38 CAC HEM A 202 1555 1555 1.96 LINK NE2 HIS A 39 FE HEM A 202 1555 1555 2.04 LINK SD MET A 79 FE HEM A 202 1555 1555 2.33 SITE 1 AC1 8 GLY A 26 THR A 64 ARG A 66 HOH A 318 SITE 2 AC1 8 HOH A 319 HOH A 338 HOH A 352 HOH A 355 SITE 1 AC2 24 HIS A 34 CYS A 35 CYS A 38 HIS A 39 SITE 2 AC2 24 ASN A 44 ILE A 47 LYS A 50 LEU A 52 SITE 3 AC2 24 ASN A 60 ILE A 62 TYR A 71 ILE A 72 SITE 4 AC2 24 GLY A 76 PRO A 77 GLY A 78 MET A 79 SITE 5 AC2 24 PRO A 80 PHE A 82 ILE A 95 HOH A 308 SITE 6 AC2 24 HOH A 314 HOH A 320 HOH A 324 HOH A 326 CRYST1 38.186 39.019 49.218 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 0.026188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020318 0.00000