HEADER OXIDOREDUCTASE 19-APR-14 4PDN TITLE CRYSTAL STRUCTURE OF E. COLI YFCM COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI KTE5; SOURCE 3 ORGANISM_TAXID: 1169326; SOURCE 4 GENE: WCE_02429; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROXYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KOBAYASHI,R.ISHII,R.ISHITANI,O.NUREKI REVDAT 4 20-MAR-24 4PDN 1 REMARK REVDAT 3 29-JAN-20 4PDN 1 SOURCE JRNL REMARK REVDAT 2 08-APR-15 4PDN 1 JRNL REVDAT 1 04-MAR-15 4PDN 0 JRNL AUTH K.KOBAYASHI,A.KATZ,A.RAJKOVIC,R.ISHII,O.E.BRANSON, JRNL AUTH 2 M.A.FREITAS,R.ISHITANI,M.IBBA,O.NUREKI JRNL TITL THE NON-CANONICAL HYDROXYLASE STRUCTURE OF YFCM REVEALS A JRNL TITL 2 METAL ION-COORDINATION MOTIF REQUIRED FOR EF-P JRNL TITL 3 HYDROXYLATION. JRNL REF NUCLEIC ACIDS RES. V. 42 12295 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 25274739 JRNL DOI 10.1093/NAR/GKU898 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 29326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1488 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 36.9290 - 3.2205 0.99 2673 148 0.1628 0.1953 REMARK 3 2 3.2205 - 2.5564 1.00 2613 146 0.1692 0.1701 REMARK 3 3 2.5564 - 2.2333 0.99 2576 140 0.1442 0.1811 REMARK 3 4 2.2333 - 2.0291 0.99 2546 152 0.1309 0.1530 REMARK 3 5 2.0291 - 1.8837 0.98 2546 136 0.1173 0.1424 REMARK 3 6 1.8837 - 1.7726 0.98 2550 126 0.1090 0.1550 REMARK 3 7 1.7726 - 1.6839 0.97 2506 148 0.1164 0.1382 REMARK 3 8 1.6839 - 1.6106 0.97 2499 127 0.1195 0.1666 REMARK 3 9 1.6106 - 1.5486 0.96 2479 117 0.1350 0.1609 REMARK 3 10 1.5486 - 1.4951 0.95 2467 117 0.1489 0.2010 REMARK 3 11 1.4951 - 1.4484 0.93 2383 131 0.1873 0.2349 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.190 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 : 0.005 1156 REMARK 3 ANGLE : 0.953 1581 REMARK 3 CHIRALITY : 0.040 166 REMARK 3 PLANARITY : 0.005 206 REMARK 3 DIHEDRAL : 13.802 395 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 4PDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29327 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.448 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.4000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM SULFATE, BIS-TRIS, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 62.18000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.48400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.18000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.48400 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 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 323 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 68 REMARK 465 LYS A 69 REMARK 465 ALA A 70 REMARK 465 ARG A 71 REMARK 465 ARG A 72 REMARK 465 GLU A 73 REMARK 465 LEU A 74 REMARK 465 VAL A 75 REMARK 465 ASP A 76 REMARK 465 PHE A 77 REMARK 465 GLY A 78 REMARK 465 TYR A 79 REMARK 465 TRP A 80 REMARK 465 TYR A 81 REMARK 465 CYS A 82 REMARK 465 PRO A 83 REMARK 465 ASP A 84 REMARK 465 GLY A 85 REMARK 465 ARG A 86 REMARK 465 ASP A 87 REMARK 465 ALA A 88 REMARK 465 GLN A 89 REMARK 465 THR A 90 REMARK 465 GLN A 91 REMARK 465 SER A 92 REMARK 465 VAL A 118 REMARK 465 SER A 119 REMARK 465 CYS A 120 REMARK 465 ASP A 121 REMARK 465 ASN A 122 REMARK 465 LEU A 123 REMARK 465 GLU A 124 REMARK 465 GLY A 125 REMARK 465 ASP A 126 REMARK 465 PHE A 127 REMARK 465 GLU A 128 REMARK 465 PRO A 129 REMARK 465 ASP A 130 REMARK 465 ALA A 180 REMARK 465 LEU A 181 REMARK 465 SER A 182 REMARK 465 LEU A 183 REMARK 465 GLU A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 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 21 CG CD OE1 OE2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 GLN A 93 CG CD OE1 NE2 REMARK 470 PHE A 94 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 GLU A 173 CG CD OE1 OE2 REMARK 470 GLU A 179 CG CD OE1 OE2 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 30 -112.16 -104.44 REMARK 500 PRO A 43 34.50 -85.43 REMARK 500 HIS A 51 153.35 67.74 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 98 OE1 REMARK 620 2 GLU A 98 OE2 55.0 REMARK 620 3 HOH A 356 O 124.4 100.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 DBREF 4PDN A 1 182 UNP L2V0E0 L2V0E0_ECOLX 1 182 SEQADV 4PDN LEU A 183 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN GLU A 184 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 185 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 186 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 187 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 188 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 189 UNP L2V0E0 EXPRESSION TAG SEQADV 4PDN HIS A 190 UNP L2V0E0 EXPRESSION TAG SEQRES 1 A 190 MET ASN SER THR HIS HIS TYR GLU GLN LEU ILE GLU ILE SEQRES 2 A 190 PHE ASN SER CYS PHE ALA ASP GLU PHE ASN THR ARG LEU SEQRES 3 A 190 ILE LYS GLY ASP ASP GLU PRO ILE TYR LEU PRO ALA ASP SEQRES 4 A 190 ALA GLU VAL PRO TYR ASN ARG ILE VAL PHE ALA HIS GLY SEQRES 5 A 190 PHE TYR ALA SER ALA ILE HIS GLU ILE SER HIS TRP CYS SEQRES 6 A 190 ILE ALA GLY LYS ALA ARG ARG GLU LEU VAL ASP PHE GLY SEQRES 7 A 190 TYR TRP TYR CYS PRO ASP GLY ARG ASP ALA GLN THR GLN SEQRES 8 A 190 SER GLN PHE GLU ASP VAL GLU VAL LYS PRO GLN ALA LEU SEQRES 9 A 190 ASP TRP LEU PHE CYS VAL ALA ALA GLY TYR PRO PHE ASN SEQRES 10 A 190 VAL SER CYS ASP ASN LEU GLU GLY ASP PHE GLU PRO ASP SEQRES 11 A 190 ARG VAL VAL PHE GLN ARG ARG VAL HIS ALA GLN VAL MET SEQRES 12 A 190 ASP TYR LEU ALA ASN GLY ILE PRO GLU ARG PRO ALA ARG SEQRES 13 A 190 PHE ILE LYS ALA LEU GLN ASN TYR TYR TYR THR PRO GLU SEQRES 14 A 190 LEU THR ALA GLU GLN PHE PRO TRP PRO GLU ALA LEU SER SEQRES 15 A 190 LEU GLU HIS HIS HIS HIS HIS HIS HET MG A 201 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *77(H2 O) HELIX 1 AA1 HIS A 6 ALA A 19 1 14 HELIX 2 AA2 PHE A 53 ALA A 67 1 15 HELIX 3 AA3 PHE A 94 GLY A 113 1 20 HELIX 4 AA4 VAL A 132 GLY A 149 1 18 HELIX 5 AA5 PRO A 151 TYR A 166 1 16 HELIX 6 AA6 THR A 171 PHE A 175 5 5 SHEET 1 AA1 3 THR A 24 LYS A 28 0 SHEET 2 AA1 3 ASN A 45 PHE A 49 1 O ILE A 47 N ILE A 27 SHEET 3 AA1 3 ILE A 34 LEU A 36 -1 N ILE A 34 O VAL A 48 LINK OE1 GLU A 98 MG MG A 201 1555 1555 2.37 LINK OE2 GLU A 98 MG MG A 201 1555 1555 2.38 LINK MG MG A 201 O HOH A 356 1555 1555 2.13 SITE 1 AC1 4 HIS A 59 HIS A 63 GLU A 98 HOH A 356 CRYST1 124.360 36.968 37.636 90.00 101.22 90.00 C 1 2 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 0.008041 0.000000 0.001595 0.00000 SCALE2 0.000000 0.027050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027088 0.00000