HEADER ISOMERASE 13-NOV-15 5ER9 TITLE STRUCTURE OF OXIDIZED UDP-GALACTOPYRANOSE MUTASE FROM MYCOBACTERIUM TITLE 2 SMEGMATIS IN COMPLEX WITH UDP IN MIXED CONFORMATION AND CLOSED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GALACTOPYRANOSE MUTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 13-412; COMPND 5 SYNONYM: UDP-GALACTOPYRANOSE MUTASE GLF; COMPND 6 EC: 5.4.99.9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 GENE: GLF, MSMEG_6404, MSMEI_6236; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMAL C5X KEYWDS GALACTOFURANOSE, ENZYME CONFORMATION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.WANGKANONT,L.L.KIESSLING,K.T.FOREST REVDAT 4 27-SEP-23 5ER9 1 REMARK REVDAT 3 11-DEC-19 5ER9 1 REMARK REVDAT 2 20-SEP-17 5ER9 1 REMARK REVDAT 1 23-NOV-16 5ER9 0 JRNL AUTH K.WANGKANONT,L.L.KIESSLING,K.T.FOREST JRNL TITL STRUCTURAL DYNAMICS OF UDP-GALACTOPYRANOSE MUTASE FROM JRNL TITL 2 MYCOBACTERIUM SMEGMATIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1690) 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 122168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 6093 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 42.5261 - 3.6382 1.00 12091 640 0.1489 0.1650 REMARK 3 2 3.6382 - 2.8879 1.00 11838 618 0.1791 0.2068 REMARK 3 3 2.8879 - 2.5229 1.00 11745 617 0.2002 0.2433 REMARK 3 4 2.5229 - 2.2923 1.00 11717 610 0.1963 0.2519 REMARK 3 5 2.2923 - 2.1280 1.00 11676 608 0.2024 0.2548 REMARK 3 6 2.1280 - 2.0025 1.00 11681 629 0.2102 0.2575 REMARK 3 7 2.0025 - 1.9022 1.00 11660 605 0.2168 0.2500 REMARK 3 8 1.9022 - 1.8194 1.00 11614 616 0.2318 0.2882 REMARK 3 9 1.8194 - 1.7494 1.00 11637 620 0.2527 0.2841 REMARK 3 10 1.7494 - 1.6890 0.90 10416 530 0.2514 0.3064 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 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 : 0.007 7462 REMARK 3 ANGLE : 1.082 10197 REMARK 3 CHIRALITY : 0.044 1034 REMARK 3 PLANARITY : 0.005 1342 REMARK 3 DIHEDRAL : 14.365 2696 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 5ER9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-14 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 122178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.689 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.81000 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: NULL REMARK 200 STARTING MODEL: 5EQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 100 MM SODIUM REMARK 280 NITRATE, 1.8 M AMMONIUM SULFATE, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 61.83750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.71300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 67.90700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 61.83750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.71300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.90700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 61.83750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.71300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.90700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 61.83750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.71300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.90700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 3 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 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 S SO4 A 507 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 ASP A 407 REMARK 465 GLU A 408 REMARK 465 SER A 409 REMARK 465 SER A 410 REMARK 465 LYS A 411 REMARK 465 ALA A 412 REMARK 465 SER B 13 REMARK 465 ASP B 407 REMARK 465 GLU B 408 REMARK 465 SER B 409 REMARK 465 SER B 410 REMARK 465 LYS B 411 REMARK 465 ALA B 412 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 OH TYR A 200 O HOH A 601 2.06 REMARK 500 O ASP A 181 O HOH A 602 2.08 REMARK 500 OD1 ASP A 247 O HOH A 603 2.10 REMARK 500 O HOH A 672 O HOH A 969 2.11 REMARK 500 OD2 ASP B 85 O HOH B 601 2.12 REMARK 500 O HOH A 787 O HOH A 1002 2.14 REMARK 500 OG SER A 119 O HOH A 605 2.15 REMARK 500 NH2 ARG A 42 O HOH A 606 2.16 REMARK 500 O HOH A 609 O HOH A 641 2.17 REMARK 500 O HOH B 848 O HOH B 987 2.18 REMARK 500 OD2 ASP B 197 O HOH B 602 2.19 REMARK 500 O HOH A 959 O HOH A 999 2.19 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 609 O HOH B 762 3656 2.16 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 GLU A 141 71.54 174.41 REMARK 500 ILE A 142 -111.14 61.38 REMARK 500 ASP A 143 -153.31 176.91 REMARK 500 GLU A 280 41.85 -87.08 REMARK 500 TYR A 375 84.63 -60.92 REMARK 500 VAL A 392 -61.13 -130.95 REMARK 500 PRO B 112 -150.29 -83.57 REMARK 500 GLU B 280 48.68 -88.55 REMARK 500 GLN B 285 -1.01 -144.79 REMARK 500 VAL B 392 -52.68 -125.21 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 A1074 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1075 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B1053 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B1054 DISTANCE = 6.45 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 509 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EQD RELATED DB: PDB REMARK 900 RELATED ID: 5EQF RELATED DB: PDB DBREF 5ER9 A 13 412 UNP A0R629 A0R629_MYCS2 13 412 DBREF 5ER9 B 13 412 UNP A0R629 A0R629_MYCS2 13 412 SEQRES 1 A 400 SER THR GLY ASN PHE ASP LEU PHE VAL VAL GLY SER GLY SEQRES 2 A 400 PHE PHE GLY LEU THR ILE ALA GLU ARG ALA ALA THR GLN SEQRES 3 A 400 LEU GLY LYS ARG VAL LEU VAL ILE GLU ARG ARG PRO HIS SEQRES 4 A 400 ILE GLY GLY ASN ALA TYR SER GLU PRO GLU PRO GLU THR SEQRES 5 A 400 GLY ILE GLU VAL HIS LYS TYR GLY ALA HIS LEU PHE HIS SEQRES 6 A 400 THR SER ASN LYS ARG VAL TRP ASP TYR VAL ARG GLN PHE SEQRES 7 A 400 THR ASP PHE THR GLY TYR GLN HIS ARG VAL PHE ALA MET SEQRES 8 A 400 HIS ASN GLY GLN ALA TYR GLN PHE PRO MET GLY LEU GLY SEQRES 9 A 400 LEU VAL SER GLN PHE PHE GLY ARG TYR PHE SER PRO ASP SEQRES 10 A 400 GLU ALA ARG ALA LEU ILE ALA GLU GLN ALA SER GLU ILE SEQRES 11 A 400 ASP THR LYS ASP ALA LYS ASN PHE GLU GLU LYS ALA ILE SEQRES 12 A 400 SER LEU VAL GLY ARG PRO LEU TYR GLU ALA PHE ILE LYS SEQRES 13 A 400 HIS TYR THR ALA LYS GLN TRP GLN THR ASP PRO LYS ASP SEQRES 14 A 400 LEU PRO ALA SER ASN ILE THR ARG LEU PRO VAL ARG TYR SEQRES 15 A 400 THR PHE ASP ASN ARG TYR PHE ASN ASP THR TYR GLU GLY SEQRES 16 A 400 LEU PRO VAL GLU GLY TYR THR LYS TRP LEU GLU ASN MET SEQRES 17 A 400 ALA ALA ASP GLU ARG ILE GLU VAL ARG LEU ASP THR ASP SEQRES 18 A 400 TRP PHE ASP VAL ARG ASP ASP LEU ARG ALA ALA ASN PRO SEQRES 19 A 400 ASP ALA PRO VAL VAL TYR THR GLY PRO LEU ASP ARG TYR SEQRES 20 A 400 PHE ASP TYR ALA GLU GLY ARG LEU GLY TRP ARG THR LEU SEQRES 21 A 400 ASP PHE GLU LEU GLU VAL LEU GLU THR GLY ASP PHE GLN SEQRES 22 A 400 GLY THR PRO VAL MET ASN TYR ASN ASP LEU ASP VAL PRO SEQRES 23 A 400 TYR THR ARG ILE HIS GLU PHE ARG HIS PHE HIS PRO GLU SEQRES 24 A 400 ARG THR TYR PRO THR ASP LYS THR VAL ILE MET ARG GLU SEQRES 25 A 400 TYR SER ARG PHE ALA ASP ASN ASP ASP GLU PRO TYR TYR SEQRES 26 A 400 PRO ILE ASN THR GLU ALA ASP ARG ALA VAL LEU ALA ALA SEQRES 27 A 400 TYR ARG ALA ARG ALA LYS ALA GLU THR ALA SER ALA LYS SEQRES 28 A 400 VAL LEU PHE GLY GLY ARG LEU GLY THR TYR GLN TYR LEU SEQRES 29 A 400 ASP MET HIS MET ALA ILE ALA SER ALA LEU SER MET PHE SEQRES 30 A 400 ASP ASN VAL LEU ALA PRO HIS LEU SER GLU GLY ALA SER SEQRES 31 A 400 LEU VAL THR GLU ASP GLU SER SER LYS ALA SEQRES 1 B 400 SER THR GLY ASN PHE ASP LEU PHE VAL VAL GLY SER GLY SEQRES 2 B 400 PHE PHE GLY LEU THR ILE ALA GLU ARG ALA ALA THR GLN SEQRES 3 B 400 LEU GLY LYS ARG VAL LEU VAL ILE GLU ARG ARG PRO HIS SEQRES 4 B 400 ILE GLY GLY ASN ALA TYR SER GLU PRO GLU PRO GLU THR SEQRES 5 B 400 GLY ILE GLU VAL HIS LYS TYR GLY ALA HIS LEU PHE HIS SEQRES 6 B 400 THR SER ASN LYS ARG VAL TRP ASP TYR VAL ARG GLN PHE SEQRES 7 B 400 THR ASP PHE THR GLY TYR GLN HIS ARG VAL PHE ALA MET SEQRES 8 B 400 HIS ASN GLY GLN ALA TYR GLN PHE PRO MET GLY LEU GLY SEQRES 9 B 400 LEU VAL SER GLN PHE PHE GLY ARG TYR PHE SER PRO ASP SEQRES 10 B 400 GLU ALA ARG ALA LEU ILE ALA GLU GLN ALA SER GLU ILE SEQRES 11 B 400 ASP THR LYS ASP ALA LYS ASN PHE GLU GLU LYS ALA ILE SEQRES 12 B 400 SER LEU VAL GLY ARG PRO LEU TYR GLU ALA PHE ILE LYS SEQRES 13 B 400 HIS TYR THR ALA LYS GLN TRP GLN THR ASP PRO LYS ASP SEQRES 14 B 400 LEU PRO ALA SER ASN ILE THR ARG LEU PRO VAL ARG TYR SEQRES 15 B 400 THR PHE ASP ASN ARG TYR PHE ASN ASP THR TYR GLU GLY SEQRES 16 B 400 LEU PRO VAL GLU GLY TYR THR LYS TRP LEU GLU ASN MET SEQRES 17 B 400 ALA ALA ASP GLU ARG ILE GLU VAL ARG LEU ASP THR ASP SEQRES 18 B 400 TRP PHE ASP VAL ARG ASP ASP LEU ARG ALA ALA ASN PRO SEQRES 19 B 400 ASP ALA PRO VAL VAL TYR THR GLY PRO LEU ASP ARG TYR SEQRES 20 B 400 PHE ASP TYR ALA GLU GLY ARG LEU GLY TRP ARG THR LEU SEQRES 21 B 400 ASP PHE GLU LEU GLU VAL LEU GLU THR GLY ASP PHE GLN SEQRES 22 B 400 GLY THR PRO VAL MET ASN TYR ASN ASP LEU ASP VAL PRO SEQRES 23 B 400 TYR THR ARG ILE HIS GLU PHE ARG HIS PHE HIS PRO GLU SEQRES 24 B 400 ARG THR TYR PRO THR ASP LYS THR VAL ILE MET ARG GLU SEQRES 25 B 400 TYR SER ARG PHE ALA ASP ASN ASP ASP GLU PRO TYR TYR SEQRES 26 B 400 PRO ILE ASN THR GLU ALA ASP ARG ALA VAL LEU ALA ALA SEQRES 27 B 400 TYR ARG ALA ARG ALA LYS ALA GLU THR ALA SER ALA LYS SEQRES 28 B 400 VAL LEU PHE GLY GLY ARG LEU GLY THR TYR GLN TYR LEU SEQRES 29 B 400 ASP MET HIS MET ALA ILE ALA SER ALA LEU SER MET PHE SEQRES 30 B 400 ASP ASN VAL LEU ALA PRO HIS LEU SER GLU GLY ALA SER SEQRES 31 B 400 LEU VAL THR GLU ASP GLU SER SER LYS ALA HET UDP A 501 25 HET FAD A 502 53 HET NO3 A 503 4 HET NO3 A 504 4 HET NO3 A 505 4 HET NO3 A 506 4 HET SO4 A 507 5 HET SO4 A 508 5 HET UDP B 501 25 HET FAD B 502 53 HET NO3 B 503 4 HET NO3 B 504 4 HET SO4 B 505 5 HET SO4 B 506 5 HET SO4 B 507 5 HET SO4 B 508 5 HET SO4 B 509 5 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM NO3 NITRATE ION HETNAM SO4 SULFATE ION FORMUL 3 UDP 2(C9 H14 N2 O12 P2) FORMUL 4 FAD 2(C27 H33 N9 O15 P2) FORMUL 5 NO3 6(N O3 1-) FORMUL 9 SO4 7(O4 S 2-) FORMUL 20 HOH *929(H2 O) HELIX 1 AA1 GLY A 25 GLY A 40 1 16 HELIX 2 AA2 GLY A 53 TYR A 57 5 5 HELIX 3 AA3 ASN A 80 ARG A 88 1 9 HELIX 4 AA4 GLY A 114 GLY A 123 1 10 HELIX 5 AA5 SER A 127 SER A 140 1 14 HELIX 6 AA6 GLU A 141 ILE A 142 5 2 HELIX 7 AA7 ASP A 143 ALA A 147 5 5 HELIX 8 AA8 ASN A 149 GLY A 159 1 11 HELIX 9 AA9 GLY A 159 ILE A 167 1 9 HELIX 10 AB1 ILE A 167 GLN A 176 1 10 HELIX 11 AB2 ASP A 178 LEU A 182 5 5 HELIX 12 AB3 PRO A 183 ILE A 187 5 5 HELIX 13 AB4 GLY A 212 ALA A 221 1 10 HELIX 14 AB5 ASP A 233 ASN A 245 1 13 HELIX 15 AB6 PRO A 255 PHE A 260 1 6 HELIX 16 AB7 ARG A 306 HIS A 309 5 4 HELIX 17 AB8 THR A 341 LYS A 363 1 23 HELIX 18 AB9 GLY A 367 TYR A 373 1 7 HELIX 19 AC1 ASP A 377 VAL A 392 1 16 HELIX 20 AC2 VAL A 392 GLY A 400 1 9 HELIX 21 AC3 GLY B 25 GLY B 40 1 16 HELIX 22 AC4 GLY B 53 ALA B 56 5 4 HELIX 23 AC5 ASN B 80 ARG B 88 1 9 HELIX 24 AC6 GLY B 114 GLY B 123 1 10 HELIX 25 AC7 SER B 127 ALA B 139 1 13 HELIX 26 AC8 ASP B 143 ALA B 147 5 5 HELIX 27 AC9 ASN B 149 GLY B 159 1 11 HELIX 28 AD1 GLY B 159 ILE B 167 1 9 HELIX 29 AD2 ILE B 167 GLN B 176 1 10 HELIX 30 AD3 ASP B 178 LEU B 182 5 5 HELIX 31 AD4 PRO B 183 LEU B 190 5 8 HELIX 32 AD5 GLY B 212 ALA B 221 1 10 HELIX 33 AD6 ASP B 233 ASN B 245 1 13 HELIX 34 AD7 PRO B 255 PHE B 260 1 6 HELIX 35 AD8 ARG B 306 HIS B 309 5 4 HELIX 36 AD9 THR B 341 LYS B 363 1 23 HELIX 37 AE1 GLY B 367 TYR B 373 1 7 HELIX 38 AE2 ASP B 377 VAL B 392 1 16 HELIX 39 AE3 VAL B 392 GLY B 400 1 9 SHEET 1 AA1 5 ILE A 226 ARG A 229 0 SHEET 2 AA1 5 VAL A 43 ILE A 46 1 N VAL A 45 O GLU A 227 SHEET 3 AA1 5 LEU A 19 VAL A 22 1 N VAL A 21 O ILE A 46 SHEET 4 AA1 5 VAL A 250 TYR A 252 1 O VAL A 251 N VAL A 22 SHEET 5 AA1 5 VAL A 364 PHE A 366 1 O LEU A 365 N VAL A 250 SHEET 1 AA2 2 GLU A 59 PRO A 60 0 SHEET 2 AA2 2 GLU A 67 VAL A 68 -1 O VAL A 68 N GLU A 59 SHEET 1 AA3 2 PHE A 76 THR A 78 0 SHEET 2 AA3 2 TYR A 205 GLY A 207 -1 O TYR A 205 N THR A 78 SHEET 1 AA4 7 GLN A 107 PHE A 111 0 SHEET 2 AA4 7 VAL A 100 HIS A 104 -1 N ALA A 102 O TYR A 109 SHEET 3 AA4 7 VAL A 289 TYR A 292 1 O ASN A 291 N PHE A 101 SHEET 4 AA4 7 ARG A 301 GLU A 304 -1 O ILE A 302 N MET A 290 SHEET 5 AA4 7 THR A 319 PHE A 328 -1 O MET A 322 N HIS A 303 SHEET 6 AA4 7 TRP A 269 LEU A 279 -1 N ASP A 273 O TYR A 325 SHEET 7 AA4 7 TYR A 337 PRO A 338 -1 O TYR A 337 N ARG A 270 SHEET 1 AA5 5 ILE B 226 ARG B 229 0 SHEET 2 AA5 5 VAL B 43 ILE B 46 1 N VAL B 45 O GLU B 227 SHEET 3 AA5 5 LEU B 19 VAL B 22 1 N VAL B 21 O ILE B 46 SHEET 4 AA5 5 VAL B 250 TYR B 252 1 O VAL B 251 N VAL B 22 SHEET 5 AA5 5 VAL B 364 PHE B 366 1 O LEU B 365 N VAL B 250 SHEET 1 AA6 2 SER B 58 PRO B 60 0 SHEET 2 AA6 2 GLU B 67 HIS B 69 -1 O VAL B 68 N GLU B 59 SHEET 1 AA7 2 PHE B 76 THR B 78 0 SHEET 2 AA7 2 TYR B 205 GLY B 207 -1 O TYR B 205 N THR B 78 SHEET 1 AA8 7 GLN B 107 GLN B 110 0 SHEET 2 AA8 7 PHE B 101 HIS B 104 -1 N ALA B 102 O TYR B 109 SHEET 3 AA8 7 VAL B 289 TYR B 292 1 O ASN B 291 N MET B 103 SHEET 4 AA8 7 ARG B 301 GLU B 304 -1 O ILE B 302 N MET B 290 SHEET 5 AA8 7 THR B 319 PHE B 328 -1 O MET B 322 N HIS B 303 SHEET 6 AA8 7 TRP B 269 LEU B 279 -1 N THR B 271 O ARG B 327 SHEET 7 AA8 7 TYR B 337 PRO B 338 -1 O TYR B 337 N ARG B 270 CISPEP 1 PHE A 111 PRO A 112 0 0.22 CISPEP 2 GLY B 15 ASN B 16 0 0.99 CISPEP 3 PHE B 111 PRO B 112 0 0.63 SITE 1 AC1 25 PHE A 111 PHE A 150 PHE A 166 ILE A 167 SITE 2 AC1 25 TYR A 170 THR A 171 GLN A 174 TRP A 175 SITE 3 AC1 25 ASN A 186 ARG A 189 LEU A 190 TYR A 200 SITE 4 AC1 25 ASN A 291 ASN A 293 ARG A 301 TYR A 337 SITE 5 AC1 25 TYR A 375 HOH A 601 HOH A 653 HOH A 672 SITE 6 AC1 25 HOH A 693 HOH A 829 HOH A 844 HOH A 874 SITE 7 AC1 25 HOH A 896 SITE 1 AC2 40 VAL A 22 GLY A 23 GLY A 25 PHE A 26 SITE 2 AC2 40 PHE A 27 ILE A 46 GLU A 47 ARG A 48 SITE 3 AC2 40 ARG A 49 GLY A 54 ASN A 55 TYR A 71 SITE 4 AC2 40 ALA A 73 HIS A 74 LEU A 75 THR A 232 SITE 5 AC2 40 ASP A 233 TRP A 234 PHE A 235 THR A 253 SITE 6 AC2 40 GLY A 254 PRO A 255 ARG A 258 LEU A 272 SITE 7 AC2 40 TYR A 336 GLY A 368 ARG A 369 TYR A 375 SITE 8 AC2 40 LEU A 376 ASP A 377 MET A 378 ALA A 381 SITE 9 AC2 40 HOH A 625 HOH A 628 HOH A 630 HOH A 719 SITE 10 AC2 40 HOH A 762 HOH A 825 HOH A 855 HOH A 861 SITE 1 AC3 7 SER A 58 GLU A 67 HIS A 69 PRO A 209 SITE 2 AC3 7 GLY A 212 TYR A 213 HIS A 309 SITE 1 AC4 4 ARG A 306 HIS A 307 HOH A 611 HOH A 760 SITE 1 AC5 8 THR A 281 GLY A 282 ASP A 283 THR A 316 SITE 2 AC5 8 HOH A 629 HOH A 747 HOH A 795 HOH B 635 SITE 1 AC6 2 ARG A 132 HOH A 698 SITE 1 AC7 3 ARG A 82 HOH A 902 HOH A 912 SITE 1 AC8 8 HIS A 104 ASN A 105 PHE A 121 GLU A 164 SITE 2 AC8 8 HOH A 627 HOH A 751 SER B 361 HOH B 781 SITE 1 AC9 25 PHE B 111 PHE B 150 PHE B 166 ILE B 167 SITE 2 AC9 25 TYR B 170 THR B 171 TRP B 175 ASN B 186 SITE 3 AC9 25 ARG B 189 LEU B 190 TYR B 200 ASN B 291 SITE 4 AC9 25 ASN B 293 ARG B 301 TYR B 337 TYR B 375 SITE 5 AC9 25 HOH B 688 HOH B 690 HOH B 728 HOH B 734 SITE 6 AC9 25 HOH B 744 HOH B 764 HOH B 799 HOH B 820 SITE 7 AC9 25 HOH B 885 SITE 1 AD1 41 VAL B 22 GLY B 23 GLY B 25 PHE B 26 SITE 2 AD1 41 PHE B 27 ILE B 46 GLU B 47 ARG B 48 SITE 3 AD1 41 ARG B 49 GLY B 54 ASN B 55 TYR B 71 SITE 4 AD1 41 ALA B 73 HIS B 74 LEU B 75 THR B 232 SITE 5 AD1 41 ASP B 233 TRP B 234 PHE B 235 THR B 253 SITE 6 AD1 41 GLY B 254 ARG B 258 LEU B 272 TYR B 336 SITE 7 AD1 41 TYR B 337 GLY B 368 ARG B 369 LEU B 370 SITE 8 AD1 41 LEU B 376 ASP B 377 MET B 378 ALA B 381 SITE 9 AD1 41 HOH B 616 HOH B 630 HOH B 662 HOH B 686 SITE 10 AD1 41 HOH B 733 HOH B 738 HOH B 765 HOH B 818 SITE 11 AD1 41 HOH B 820 SITE 1 AD2 7 SER B 58 GLU B 67 HIS B 69 PRO B 209 SITE 2 AD2 7 GLY B 212 TYR B 213 HIS B 309 SITE 1 AD3 1 ARG B 132 SITE 1 AD4 4 LYS B 81 ASP B 85 ARG B 88 HOH B 919 SITE 1 AD5 2 ALA B 263 ARG B 354 SITE 1 AD6 4 PRO B 183 ALA B 184 SER B 185 HOH B 642 SITE 1 AD7 7 HOH A 706 GLN B 97 ARG B 199 HOH B 605 SITE 2 AD7 7 HOH B 745 HOH B 843 HOH B 903 SITE 1 AD8 2 ARG B 124 HOH B 798 CRYST1 123.675 131.426 135.814 90.00 90.00 90.00 I 2 2 2 16 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 0.008086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007363 0.00000