HEADER OXIDOREDUCTASE 03-DEC-13 4NUB TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI RIBOSOMAL OXYGENASE YCFD COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBOSOMAL OXYGENASE YCFD, ROX; COMPND 5 EC: 1.14.11.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B1128, JW1114, YCFD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DL41 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS STRUCTURAL GENOMICS, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS KEYWDS 2 INITIATIVE, BSGI, JELLY ROLL, CUPIN, BETA-BARREL, 2OG/FE2+ DEPENDENT KEYWDS 3 OXYGENASE, RIBOSOMAL PROTEIN L-16, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.M.VAN STAALDUINEN,Z.JIA,MONTREAL-KINGSTON BACTERIAL STRUCTURAL AUTHOR 2 GENOMICS INITIATIVE (BSGI) REVDAT 3 22-NOV-17 4NUB 1 REMARK REVDAT 2 30-APR-14 4NUB 1 JRNL REVDAT 1 26-FEB-14 4NUB 0 JRNL AUTH L.M.VAN STAALDUINEN,S.K.NOVAKOWSKI,Z.JIA JRNL TITL STRUCTURE AND FUNCTIONAL ANALYSIS OF YCFD, A NOVEL JRNL TITL 2 2-OXOGLUTARATE/FE(2+)-DEPENDENT OXYGENASE INVOLVED IN JRNL TITL 3 TRANSLATIONAL REGULATION IN ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 426 1898 2014 JRNL REFN ISSN 0022-2836 JRNL PMID 24530688 JRNL DOI 10.1016/J.JMB.2014.02.008 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 893 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 19.9266 - 4.8862 1.00 2979 143 0.1594 0.1964 REMARK 3 2 4.8862 - 3.8877 1.00 2845 125 0.1400 0.1830 REMARK 3 3 3.8877 - 3.3991 1.00 2752 153 0.1783 0.2352 REMARK 3 4 3.3991 - 3.0895 1.00 2740 153 0.2035 0.2444 REMARK 3 5 3.0895 - 2.8688 1.00 2712 149 0.2598 0.2974 REMARK 3 6 2.8688 - 2.7001 1.00 2681 170 0.3075 0.3878 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.310 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 : 0.009 2977 REMARK 3 ANGLE : 1.218 4056 REMARK 3 CHIRALITY : 0.086 418 REMARK 3 PLANARITY : 0.006 541 REMARK 3 DIHEDRAL : 15.441 1089 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9133 14.9265 84.3808 REMARK 3 T TENSOR REMARK 3 T11: 0.1566 T22: 0.2272 REMARK 3 T33: 0.1773 T12: 0.0822 REMARK 3 T13: 0.0206 T23: 0.0372 REMARK 3 L TENSOR REMARK 3 L11: 0.1548 L22: 0.3824 REMARK 3 L33: 0.6056 L12: 0.0213 REMARK 3 L13: -0.0631 L23: 0.0713 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: 0.0169 S13: 0.0096 REMARK 3 S21: 0.0853 S22: 0.1747 S23: -0.0775 REMARK 3 S31: -0.0689 S32: -0.4677 S33: 0.0670 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 259 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6204 -0.9651 57.1806 REMARK 3 T TENSOR REMARK 3 T11: 0.2324 T22: 0.2259 REMARK 3 T33: 0.2210 T12: -0.1426 REMARK 3 T13: -0.0138 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 0.2007 L22: 0.0113 REMARK 3 L33: 0.2468 L12: -0.1125 REMARK 3 L13: 0.3371 L23: -0.0643 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: 0.0616 S13: -0.0254 REMARK 3 S21: -0.0584 S22: 0.2824 S23: 0.1080 REMARK 3 S31: -0.1799 S32: 0.1305 S33: 0.0917 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 260 THROUGH 372 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0713 24.2904 58.7946 REMARK 3 T TENSOR REMARK 3 T11: -0.0802 T22: 0.0140 REMARK 3 T33: 0.2055 T12: -0.3670 REMARK 3 T13: 0.0367 T23: 0.0518 REMARK 3 L TENSOR REMARK 3 L11: 0.1332 L22: 0.1787 REMARK 3 L33: 0.1563 L12: 0.1131 REMARK 3 L13: 0.0188 L23: -0.0538 REMARK 3 S TENSOR REMARK 3 S11: -0.1379 S12: 0.2331 S13: -0.0599 REMARK 3 S21: -0.1447 S22: 0.2893 S23: -0.0812 REMARK 3 S31: 0.1023 S32: -0.2415 S33: 0.2413 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 4NUB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97913, 0.97927, 0.91837 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31993 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.6% PEG 4000, 30% GLYCEROL, 0.07M REMARK 280 SODIUM ACETATE, 0.5 UL OF 1/10 DILUTION OF SEED SOLUTION, PH 4.6, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 105.44900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.86550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.86550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 158.17350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.86550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.86550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.72450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.86550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.86550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 158.17350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.86550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.86550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.72450 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 105.44900 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 300 REMARK: BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE MONOMER REMARK 300 IN THE ASYMMETRIC UNIT BY THE OPERATION -Y,-X,-Z+1/2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 105.44900 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 GLN A 149 REMARK 465 MSE A 150 REMARK 465 LYS A 151 REMARK 465 GLN A 152 REMARK 465 HIS A 153 REMARK 465 CYS A 154 REMARK 465 PRO A 155 REMARK 465 HIS A 156 REMARK 465 PRO A 157 REMARK 465 ASP A 158 REMARK 465 LEU A 159 REMARK 465 GLY A 373 REMARK 465 SER A 374 REMARK 465 GLY A 375 REMARK 465 ARG A 376 REMARK 465 VAL A 377 REMARK 465 GLU A 378 REMARK 465 HIS A 379 REMARK 465 HIS A 380 REMARK 465 HIS A 381 REMARK 465 HIS A 382 REMARK 465 HIS A 383 REMARK 465 HIS A 384 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 14 OE1 OE2 REMARK 470 GLN A 57 CD OE1 NE2 REMARK 470 ASP A 58 OD1 OD2 REMARK 470 LYS A 60 CG CD CE NZ REMARK 470 GLN A 62 OE1 NE2 REMARK 470 GLU A 69 CG CD OE1 OE2 REMARK 470 HIS A 73 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 128 OE1 REMARK 470 LEU A 160 CG CD1 CD2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 GLN A 220 CD OE1 NE2 REMARK 470 ASP A 326 CG OD1 OD2 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 508 O HOH A 509 2.11 REMARK 500 O HOH A 509 O HOH A 513 2.17 REMARK 500 O HOH A 525 O HOH A 526 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 LEU A 7 138.20 -171.07 REMARK 500 HIS A 16 -50.71 -122.35 REMARK 500 LYS A 19 -52.42 -129.86 REMARK 500 ASP A 58 16.88 54.95 REMARK 500 PRO A 67 -167.93 -75.41 REMARK 500 GLU A 69 -71.10 -67.86 REMARK 500 ASP A 72 -166.64 -126.01 REMARK 500 ASP A 109 -117.38 -98.10 REMARK 500 ASP A 110 -158.81 -129.38 REMARK 500 ASP A 232 50.05 -115.56 REMARK 500 PRO A 287 152.87 -48.23 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 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 125 NE2 REMARK 620 2 HIS A 187 NE2 73.1 REMARK 620 3 ASP A 127 OD2 116.2 84.6 REMARK 620 4 HOH A 513 O 160.6 115.8 82.6 REMARK 620 5 HOH A 508 O 88.4 103.8 155.4 72.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 402 DBREF 4NUB A 1 373 UNP P27431 YCFD_ECOLI 1 373 SEQADV 4NUB ALA A 146 UNP P27431 GLU 146 ENGINEERED MUTATION SEQADV 4NUB ALA A 147 UNP P27431 LYS 147 ENGINEERED MUTATION SEQADV 4NUB SER A 374 UNP P27431 EXPRESSION TAG SEQADV 4NUB GLY A 375 UNP P27431 EXPRESSION TAG SEQADV 4NUB ARG A 376 UNP P27431 EXPRESSION TAG SEQADV 4NUB VAL A 377 UNP P27431 EXPRESSION TAG SEQADV 4NUB GLU A 378 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 379 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 380 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 381 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 382 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 383 UNP P27431 EXPRESSION TAG SEQADV 4NUB HIS A 384 UNP P27431 EXPRESSION TAG SEQRES 1 A 384 MSE GLU TYR GLN LEU THR LEU ASN TRP PRO ASP PHE LEU SEQRES 2 A 384 GLU ARG HIS TRP GLN LYS ARG PRO VAL VAL LEU LYS ARG SEQRES 3 A 384 GLY PHE ASN ASN PHE ILE ASP PRO ILE SER PRO ASP GLU SEQRES 4 A 384 LEU ALA GLY LEU ALA MSE GLU SER GLU VAL ASP SER ARG SEQRES 5 A 384 LEU VAL SER HIS GLN ASP GLY LYS TRP GLN VAL SER HIS SEQRES 6 A 384 GLY PRO PHE GLU SER TYR ASP HIS LEU GLY GLU THR ASN SEQRES 7 A 384 TRP SER LEU LEU VAL GLN ALA VAL ASN HIS TRP HIS GLU SEQRES 8 A 384 PRO THR ALA ALA LEU MSE ARG PRO PHE ARG GLU LEU PRO SEQRES 9 A 384 ASP TRP ARG ILE ASP ASP LEU MSE ILE SER PHE SER VAL SEQRES 10 A 384 PRO GLY GLY GLY VAL GLY PRO HIS LEU ASP GLN TYR ASP SEQRES 11 A 384 VAL PHE ILE ILE GLN GLY THR GLY ARG ARG ARG TRP ARG SEQRES 12 A 384 VAL GLY ALA ALA LEU GLN MSE LYS GLN HIS CYS PRO HIS SEQRES 13 A 384 PRO ASP LEU LEU GLN VAL ASP PRO PHE GLU ALA ILE ILE SEQRES 14 A 384 ASP GLU GLU LEU GLU PRO GLY ASP ILE LEU TYR ILE PRO SEQRES 15 A 384 PRO GLY PHE PRO HIS GLU GLY TYR ALA LEU GLU ASN ALA SEQRES 16 A 384 MSE ASN TYR SER VAL GLY PHE ARG ALA PRO ASN THR ARG SEQRES 17 A 384 GLU LEU ILE SER GLY PHE ALA ASP TYR VAL LEU GLN ARG SEQRES 18 A 384 GLU LEU GLY GLY ASN TYR TYR SER ASP PRO ASP VAL PRO SEQRES 19 A 384 PRO ARG ALA HIS PRO ALA ASP VAL LEU PRO GLN GLU MSE SEQRES 20 A 384 ASP LYS LEU ARG GLU MSE MSE LEU GLU LEU ILE ASN GLN SEQRES 21 A 384 PRO GLU HIS PHE LYS GLN TRP PHE GLY GLU PHE ILE SER SEQRES 22 A 384 GLN SER ARG HIS GLU LEU ASP ILE ALA PRO PRO GLU PRO SEQRES 23 A 384 PRO TYR GLN PRO ASP GLU ILE TYR ASP ALA LEU LYS GLN SEQRES 24 A 384 GLY GLU VAL LEU VAL ARG LEU GLY GLY LEU ARG VAL LEU SEQRES 25 A 384 ARG ILE GLY ASP ASP VAL TYR ALA ASN GLY GLU LYS ILE SEQRES 26 A 384 ASP SER PRO HIS ARG PRO ALA LEU ASP ALA LEU ALA SER SEQRES 27 A 384 ASN ILE ALA LEU THR ALA GLU ASN PHE GLY ASP ALA LEU SEQRES 28 A 384 GLU ASP PRO SER PHE LEU ALA MSE LEU ALA ALA LEU VAL SEQRES 29 A 384 ASN SER GLY TYR TRP PHE PHE GLU GLY SER GLY ARG VAL SEQRES 30 A 384 GLU HIS HIS HIS HIS HIS HIS MODRES 4NUB MSE A 1 MET SELENOMETHIONINE MODRES 4NUB MSE A 45 MET SELENOMETHIONINE MODRES 4NUB MSE A 97 MET SELENOMETHIONINE MODRES 4NUB MSE A 112 MET SELENOMETHIONINE MODRES 4NUB MSE A 196 MET SELENOMETHIONINE MODRES 4NUB MSE A 247 MET SELENOMETHIONINE MODRES 4NUB MSE A 253 MET SELENOMETHIONINE MODRES 4NUB MSE A 254 MET SELENOMETHIONINE MODRES 4NUB MSE A 359 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 45 8 HET MSE A 97 8 HET MSE A 112 8 HET MSE A 196 8 HET MSE A 247 8 HET MSE A 253 8 HET MSE A 254 8 HET MSE A 359 8 HET FE A 401 1 HET GOL A 402 6 HETNAM MSE SELENOMETHIONINE HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 FE FE 3+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *51(H2 O) HELIX 1 1 ASN A 8 HIS A 16 1 9 HELIX 2 2 SER A 36 MSE A 45 1 10 HELIX 3 3 ALA A 85 TRP A 89 5 5 HELIX 4 4 PRO A 92 ARG A 101 5 10 HELIX 5 5 ASN A 206 ARG A 221 1 16 HELIX 6 6 LEU A 243 ASN A 259 1 17 HELIX 7 7 GLU A 262 SER A 273 1 12 HELIX 8 8 GLN A 289 GLN A 299 1 11 HELIX 9 9 HIS A 329 ASN A 339 1 11 HELIX 10 10 THR A 343 GLU A 352 5 10 HELIX 11 11 ASP A 353 GLY A 367 1 15 SHEET 1 A 8 VAL A 22 LEU A 24 0 SHEET 2 A 8 ILE A 178 ILE A 181 -1 O ILE A 178 N LEU A 24 SHEET 3 A 8 VAL A 131 GLN A 135 -1 N ILE A 133 O LEU A 179 SHEET 4 A 8 ALA A 195 PHE A 202 -1 O TYR A 198 N ILE A 134 SHEET 5 A 8 ILE A 108 SER A 116 -1 N MSE A 112 O SER A 199 SHEET 6 A 8 TRP A 79 VAL A 83 -1 N LEU A 81 O PHE A 115 SHEET 7 A 8 SER A 51 GLN A 57 -1 N VAL A 54 O SER A 80 SHEET 8 A 8 LYS A 60 HIS A 65 -1 O SER A 64 N LEU A 53 SHEET 1 B 3 ILE A 169 LEU A 173 0 SHEET 2 B 3 ARG A 140 VAL A 144 -1 N TRP A 142 O GLU A 171 SHEET 3 B 3 HIS A 187 ALA A 191 -1 O GLU A 188 N ARG A 143 SHEET 1 C 3 ALA A 341 LEU A 342 0 SHEET 2 C 3 LEU A 303 ARG A 305 -1 N LEU A 303 O LEU A 342 SHEET 3 C 3 TRP A 369 PHE A 371 -1 O PHE A 370 N VAL A 304 SHEET 1 D 3 VAL A 311 ILE A 314 0 SHEET 2 D 3 ASP A 317 ALA A 320 -1 O TYR A 319 N LEU A 312 SHEET 3 D 3 GLU A 323 ILE A 325 -1 O ILE A 325 N VAL A 318 LINK C MSE A 1 N GLU A 2 1555 1555 1.33 LINK C ALA A 44 N MSE A 45 1555 1555 1.33 LINK C MSE A 45 N GLU A 46 1555 1555 1.33 LINK C LEU A 96 N MSE A 97 1555 1555 1.33 LINK C MSE A 97 N ARG A 98 1555 1555 1.33 LINK C LEU A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N ILE A 113 1555 1555 1.33 LINK C ALA A 195 N MSE A 196 1555 1555 1.33 LINK C MSE A 196 N ASN A 197 1555 1555 1.33 LINK C GLU A 246 N MSE A 247 1555 1555 1.33 LINK C MSE A 247 N ASP A 248 1555 1555 1.33 LINK C GLU A 252 N MSE A 253 1555 1555 1.33 LINK C MSE A 253 N MSE A 254 1555 1555 1.33 LINK C MSE A 254 N LEU A 255 1555 1555 1.33 LINK C ALA A 358 N MSE A 359 1555 1555 1.33 LINK C MSE A 359 N LEU A 360 1555 1555 1.33 LINK NE2 HIS A 125 FE FE A 401 1555 1555 2.03 LINK NE2 HIS A 187 FE FE A 401 1555 1555 2.18 LINK OD2 ASP A 127 FE FE A 401 1555 1555 2.21 LINK FE FE A 401 O HOH A 513 1555 1555 2.48 LINK FE FE A 401 O HOH A 508 1555 1555 2.57 CISPEP 1 GLY A 66 PRO A 67 0 -2.87 CISPEP 2 GLU A 285 PRO A 286 0 -7.47 SITE 1 AC1 5 HIS A 125 ASP A 127 HIS A 187 HOH A 508 SITE 2 AC1 5 HOH A 513 SITE 1 AC2 6 LEU A 7 ASN A 8 PHE A 12 HIS A 16 SITE 2 AC2 6 GLU A 301 GLU A 372 CRYST1 75.731 75.731 210.898 90.00 90.00 90.00 P 43 21 2 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 0.013205 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004742 0.00000 HETATM 1 N MSE A 1 18.467 29.696 81.804 1.00 88.41 N ANISOU 1 N MSE A 1 11430 10447 11714 749 222 -391 N HETATM 2 CA MSE A 1 18.872 28.652 82.743 1.00 87.68 C ANISOU 2 CA MSE A 1 11322 10362 11630 722 161 -411 C HETATM 3 C MSE A 1 18.697 27.267 82.111 1.00 82.75 C ANISOU 3 C MSE A 1 10694 9771 10976 702 134 -400 C HETATM 4 O MSE A 1 17.985 27.127 81.123 1.00 81.07 O ANISOU 4 O MSE A 1 10463 9577 10761 707 168 -379 O HETATM 5 CB MSE A 1 18.062 28.759 84.038 1.00 86.96 C ANISOU 5 CB MSE A 1 11207 10277 11557 744 183 -389 C HETATM 6 CG MSE A 1 18.618 27.936 85.190 1.00 88.82 C ANISOU 6 CG MSE A 1 11418 10505 11825 705 136 -410 C HETATM 7 SE MSE A 1 17.238 27.034 86.243 0.61130.71 SE ANISOU 7 SE MSE A 1 16698 15839 17125 727 168 -356 SE HETATM 8 CE MSE A 1 18.347 25.623 87.035 1.00 72.03 C ANISOU 8 CE MSE A 1 9225 8374 9771 629 173 -363 C