HEADER OXIDOREDUCTASE 28-FEB-14 4PQ1 TITLE CRYSTAL STRUCTURE AND FUNCTIONAL IMPLICATIONS OF A DSBF HOMOLOGUE FROM TITLE 2 CORYNEBACTERIUM DIPHTHERIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ELECTRON TRANSPORT RELATED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 29-186; COMPND 5 SYNONYM: DSBF; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 257309; SOURCE 4 STRAIN: NCTC 13129; SOURCE 5 GENE: DIP0411; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THIOREDOXIN-LIKE REGION, REDUCTANT, OXIDANT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.H.UM,J.S.KIM,B.Y.YOON,N.C.HA REVDAT 3 01-JAN-20 4PQ1 1 JRNL REVDAT 2 22-NOV-17 4PQ1 1 REMARK REVDAT 1 10-SEP-14 4PQ1 0 JRNL AUTH S.H.UM,J.S.KIM,K.LEE,N.C.HA JRNL TITL STRUCTURE OF A DSBF HOMOLOGUE FROM CORYNEBACTERIUM JRNL TITL 2 DIPHTHERIAE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 70 1167 2014 JRNL REFN ESSN 2053-230X JRNL PMID 25195886 JRNL DOI 10.1107/S2053230X14016355 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 17168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 914 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 36.1862 - 4.0092 0.99 2691 143 0.1385 0.2065 REMARK 3 2 4.0092 - 3.1828 0.99 2647 125 0.1599 0.2306 REMARK 3 3 3.1828 - 2.7807 0.96 2487 144 0.1852 0.2359 REMARK 3 4 2.7807 - 2.5265 0.93 2454 132 0.2176 0.2828 REMARK 3 5 2.5265 - 2.3454 0.91 2341 148 0.2301 0.3069 REMARK 3 6 2.3454 - 2.2072 0.88 2310 109 0.2662 0.3046 REMARK 3 7 2.2072 - 2.0967 0.86 2238 113 0.2827 0.3412 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.04 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 : 0.008 2515 REMARK 3 ANGLE : 1.088 3426 REMARK 3 CHIRALITY : 0.042 383 REMARK 3 PLANARITY : 0.006 452 REMARK 3 DIHEDRAL : 14.193 916 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 4PQ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085079. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18081 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.097 REMARK 200 RESOLUTION RANGE LOW (A) : 36.181 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.0 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: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 30% PEG 4K, PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287.15K 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 18.08100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 SER A 186 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 OD1 ASP A 92 O HOH A 268 2.17 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 SER A 35 121.19 -35.79 REMARK 500 SER A 53 -178.06 -64.77 REMARK 500 LEU A 170 50.93 -97.38 REMARK 500 ASP B 72 15.26 57.21 REMARK 500 LEU B 170 45.23 -96.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 4PQ1 A 29 186 UNP Q6NJJ0 Q6NJJ0_CORDI 29 186 DBREF 4PQ1 B 29 186 UNP Q6NJJ0 Q6NJJ0_CORDI 29 186 SEQRES 1 A 158 GLY THR PHE GLN PHE HIS SER PRO GLY GLY LYS THR GLU SEQRES 2 A 158 ILE PHE TYR ASP GLU GLY GLU ARG ALA PRO VAL SER GLU SEQRES 3 A 158 ILE ARG GLY GLU GLY LEU THR SER ASP SER VAL SER LEU SEQRES 4 A 158 ALA ASP TYR LYS ASP LYS ILE VAL VAL LEU ASN ALA TRP SEQRES 5 A 158 GLY GLN TRP CYS ALA PRO CYS ARG SER GLU SER ASP ASP SEQRES 6 A 158 LEU GLN GLU VAL HIS GLU TYR LEU GLY ASP LYS GLY THR SEQRES 7 A 158 VAL VAL GLY ILE ASN VAL ARG ASP TYR SER LYS ASN ILE SEQRES 8 A 158 ALA GLN ASP PHE VAL LYS ASP ASN GLY ILE THR TYR PRO SEQRES 9 A 158 SER ILE TYR ASP PRO PRO PHE LYS THR ALA ALA GLN LEU SEQRES 10 A 158 GLY GLY VAL PRO ALA SER VAL VAL PRO THR THR ILE VAL SEQRES 11 A 158 LEU ASP LYS GLN HIS ARG PRO ALA ALA VAL PHE LEU ARG SEQRES 12 A 158 GLU VAL THR ALA GLN ASP LEU ILE LYS VAL ILE ASP SER SEQRES 13 A 158 LEU SER SEQRES 1 B 158 GLY THR PHE GLN PHE HIS SER PRO GLY GLY LYS THR GLU SEQRES 2 B 158 ILE PHE TYR ASP GLU GLY GLU ARG ALA PRO VAL SER GLU SEQRES 3 B 158 ILE ARG GLY GLU GLY LEU THR SER ASP SER VAL SER LEU SEQRES 4 B 158 ALA ASP TYR LYS ASP LYS ILE VAL VAL LEU ASN ALA TRP SEQRES 5 B 158 GLY GLN TRP CYS ALA PRO CYS ARG SER GLU SER ASP ASP SEQRES 6 B 158 LEU GLN GLU VAL HIS GLU TYR LEU GLY ASP LYS GLY THR SEQRES 7 B 158 VAL VAL GLY ILE ASN VAL ARG ASP TYR SER LYS ASN ILE SEQRES 8 B 158 ALA GLN ASP PHE VAL LYS ASP ASN GLY ILE THR TYR PRO SEQRES 9 B 158 SER ILE TYR ASP PRO PRO PHE LYS THR ALA ALA GLN LEU SEQRES 10 B 158 GLY GLY VAL PRO ALA SER VAL VAL PRO THR THR ILE VAL SEQRES 11 B 158 LEU ASP LYS GLN HIS ARG PRO ALA ALA VAL PHE LEU ARG SEQRES 12 B 158 GLU VAL THR ALA GLN ASP LEU ILE LYS VAL ILE ASP SER SEQRES 13 B 158 LEU SER FORMUL 3 HOH *149(H2 O) HELIX 1 1 ASP A 45 ARG A 49 5 5 HELIX 2 2 ALA A 68 LYS A 71 5 4 HELIX 3 3 CYS A 84 GLU A 90 1 7 HELIX 4 4 GLU A 90 GLY A 102 1 13 HELIX 5 5 SER A 116 ASN A 127 1 12 HELIX 6 6 LYS A 140 LEU A 145 1 6 HELIX 7 7 THR A 174 LEU A 185 1 12 HELIX 8 8 ASP B 45 ARG B 49 5 5 HELIX 9 9 ALA B 68 LYS B 71 5 4 HELIX 10 10 CYS B 84 GLY B 102 1 19 HELIX 11 11 SER B 116 ASN B 127 1 12 HELIX 12 12 PHE B 139 ALA B 143 5 5 HELIX 13 13 THR B 174 SER B 184 1 11 SHEET 1 A 6 GLU A 41 PHE A 43 0 SHEET 2 A 6 PRO A 165 PHE A 169 -1 O VAL A 168 N ILE A 42 SHEET 3 A 6 THR A 155 LEU A 159 -1 N VAL A 158 O ALA A 166 SHEET 4 A 6 ILE A 74 TRP A 80 -1 N LEU A 77 O ILE A 157 SHEET 5 A 6 GLY A 105 ASN A 111 1 O ILE A 110 N ASN A 78 SHEET 6 A 6 SER A 133 TYR A 135 1 O ILE A 134 N GLY A 109 SHEET 1 B 2 ARG A 56 GLU A 58 0 SHEET 2 B 2 SER A 64 SER A 66 -1 O VAL A 65 N GLY A 57 SHEET 1 C 6 GLU B 41 PHE B 43 0 SHEET 2 C 6 PRO B 165 PHE B 169 -1 O VAL B 168 N ILE B 42 SHEET 3 C 6 THR B 155 LEU B 159 -1 N THR B 156 O PHE B 169 SHEET 4 C 6 ILE B 74 TRP B 80 -1 N LEU B 77 O ILE B 157 SHEET 5 C 6 GLY B 105 ASN B 111 1 O VAL B 108 N VAL B 76 SHEET 6 C 6 SER B 133 TYR B 135 1 O ILE B 134 N GLY B 109 SHEET 1 D 2 ARG B 56 GLU B 58 0 SHEET 2 D 2 SER B 64 SER B 66 -1 O VAL B 65 N GLY B 57 SSBOND 1 CYS A 84 CYS A 87 1555 1555 2.11 CISPEP 1 VAL A 153 PRO A 154 0 3.80 CISPEP 2 VAL B 153 PRO B 154 0 -0.47 CRYST1 78.103 36.162 62.522 90.00 67.89 90.00 P 1 21 1 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 0.012804 0.000000 -0.005202 0.00000 SCALE2 0.000000 0.027653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017264 0.00000