HEADER TRANSFERASE/INHIBITOR 10-FEB-21 7LOV TITLE CRYSTAL STRUCTURE OF CLOSTRIDIUM DIFFICILE TOXIN B (TCDB) TITLE 2 GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP AND NOEUROMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN B; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.22.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 3 ORGANISM_COMMON: PEPTOCLOSTRIDIUM DIFFICILE; SOURCE 4 ORGANISM_TAXID: 1496; SOURCE 5 GENE: TCDB, TOXB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITORS, TCDB, TOXIN, KINETIC ISOTOPE EFFECTS, KIES, DRUG DESIGN, KEYWDS 2 TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.K.HARIJAN,A.S.PAPARELLA,B.L.ABOULACHE,J.B.BONANNO,S.C.ALMO, AUTHOR 2 V.L.SCHRAMM REVDAT 2 18-OCT-23 7LOV 1 REMARK REVDAT 1 17-NOV-21 7LOV 0 JRNL AUTH A.S.PAPARELLA,B.L.ABOULACHE,R.K.HARIJAN,K.S.POTTS,P.C.TYLER, JRNL AUTH 2 V.L.SCHRAMM JRNL TITL INHIBITION OF CLOSTRIDIUM DIFFICILE TCDA AND TCDB TOXINS JRNL TITL 2 WITH TRANSITION STATE ANALOGUES. JRNL REF NAT COMMUN V. 12 6285 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34725358 JRNL DOI 10.1038/S41467-021-26580-6 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2334 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3402 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8808 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.50000 REMARK 3 B22 (A**2) : -1.21000 REMARK 3 B33 (A**2) : -1.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.506 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.279 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.244 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.792 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9068 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 8163 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12242 ; 1.219 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 19059 ; 1.125 ; 1.581 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1075 ; 5.779 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 517 ;35.275 ;24.758 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1664 ;15.513 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.530 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1193 ; 0.044 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 10034 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1819 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 538 B 2 538 18364 0.060 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7LOV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48863 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 28.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.27000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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: 5UQM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85 MM SODIUM CITRATE PH 5.6, 170 MM REMARK 280 AMMONIUM ACETATE, 25.5 % (W/V) PEG 4000, 15 %(V/V) GLYCEROL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 76.29450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.33800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.29450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.33800 REMARK 290 SMTRY3 4 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 MET A 0 REMARK 465 GLY A 1 REMARK 465 GLY A 541 REMARK 465 SER A 542 REMARK 465 LEU A 543 REMARK 465 LEU A 544 REMARK 465 GLU A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 HIS A 548 REMARK 465 HIS A 549 REMARK 465 HIS A 550 REMARK 465 HIS A 551 REMARK 465 MET B 0 REMARK 465 GLY B 1 REMARK 465 GLU B 540 REMARK 465 GLY B 541 REMARK 465 SER B 542 REMARK 465 LEU B 543 REMARK 465 LEU B 544 REMARK 465 GLU B 545 REMARK 465 HIS B 546 REMARK 465 HIS B 547 REMARK 465 HIS B 548 REMARK 465 HIS B 549 REMARK 465 HIS B 550 REMARK 465 HIS B 551 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 MET A 448 CG SD CE REMARK 470 ARG B 16 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 161 CG CD1 CD2 REMARK 470 ASN B 162 CG OD1 ND2 REMARK 470 PHE B 166 CG CD1 CD2 CE1 CE2 CZ 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 TYR A 63 76.09 -113.79 REMARK 500 ARG A 158 -62.22 -29.43 REMARK 500 ASN A 160 46.01 -80.86 REMARK 500 ILE A 359 -62.30 -96.72 REMARK 500 LEU A 468 -63.34 -90.76 REMARK 500 GLN B 20 96.41 -69.62 REMARK 500 TYR B 63 76.30 -114.11 REMARK 500 ASN B 160 44.44 -83.92 REMARK 500 ILE B 359 -63.08 -96.46 REMARK 500 LEU B 468 -62.97 -90.93 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 MN A 606 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 288 OD2 REMARK 620 2 GLU A 515 OE1 82.3 REMARK 620 3 UDP A 602 O1A 79.6 161.3 REMARK 620 4 UDP A 602 O2B 161.4 115.9 82.5 REMARK 620 5 HOH A 708 O 94.7 79.5 97.6 92.5 REMARK 620 6 HOH A 733 O 87.8 94.3 89.4 87.0 172.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 605 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 288 OD2 REMARK 620 2 GLU B 515 OE1 86.3 REMARK 620 3 UDP B 602 O1A 78.8 165.0 REMARK 620 4 UDP B 602 O3B 160.3 113.4 81.5 REMARK 620 5 HOH B 709 O 96.5 77.3 102.2 89.3 REMARK 620 6 HOH B 718 O 92.9 93.3 89.5 85.2 166.2 REMARK 620 N 1 2 3 4 5 DBREF 7LOV A 2 545 UNP P18177 TCDB_CLODI 2 545 DBREF 7LOV B 2 545 UNP P18177 TCDB_CLODI 2 545 SEQADV 7LOV MET A 0 UNP P18177 EXPRESSION TAG SEQADV 7LOV GLY A 1 UNP P18177 EXPRESSION TAG SEQADV 7LOV LEU A 544 UNP P18177 GLY 544 CONFLICT SEQADV 7LOV HIS A 546 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS A 547 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS A 548 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS A 549 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS A 550 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS A 551 UNP P18177 EXPRESSION TAG SEQADV 7LOV MET B 0 UNP P18177 EXPRESSION TAG SEQADV 7LOV GLY B 1 UNP P18177 EXPRESSION TAG SEQADV 7LOV LEU B 544 UNP P18177 GLY 544 CONFLICT SEQADV 7LOV HIS B 546 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS B 547 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS B 548 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS B 549 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS B 550 UNP P18177 EXPRESSION TAG SEQADV 7LOV HIS B 551 UNP P18177 EXPRESSION TAG SEQRES 1 A 552 MET GLY SER LEU VAL ASN ARG LYS GLN LEU GLU LYS MET SEQRES 2 A 552 ALA ASN VAL ARG PHE ARG THR GLN GLU ASP GLU TYR VAL SEQRES 3 A 552 ALA ILE LEU ASP ALA LEU GLU GLU TYR HIS ASN MET SER SEQRES 4 A 552 GLU ASN THR VAL VAL GLU LYS TYR LEU LYS LEU LYS ASP SEQRES 5 A 552 ILE ASN SER LEU THR ASP ILE TYR ILE ASP THR TYR LYS SEQRES 6 A 552 LYS SER GLY ARG ASN LYS ALA LEU LYS LYS PHE LYS GLU SEQRES 7 A 552 TYR LEU VAL THR GLU VAL LEU GLU LEU LYS ASN ASN ASN SEQRES 8 A 552 LEU THR PRO VAL GLU LYS ASN LEU HIS PHE VAL TRP ILE SEQRES 9 A 552 GLY GLY GLN ILE ASN ASP THR ALA ILE ASN TYR ILE ASN SEQRES 10 A 552 GLN TRP LYS ASP VAL ASN SER ASP TYR ASN VAL ASN VAL SEQRES 11 A 552 PHE TYR ASP SER ASN ALA PHE LEU ILE ASN THR LEU LYS SEQRES 12 A 552 LYS THR VAL VAL GLU SER ALA ILE ASN ASP THR LEU GLU SEQRES 13 A 552 SER PHE ARG GLU ASN LEU ASN ASP PRO ARG PHE ASP TYR SEQRES 14 A 552 ASN LYS PHE PHE ARG LYS ARG MET GLU ILE ILE TYR ASP SEQRES 15 A 552 LYS GLN LYS ASN PHE ILE ASN TYR TYR LYS ALA GLN ARG SEQRES 16 A 552 GLU GLU ASN PRO GLU LEU ILE ILE ASP ASP ILE VAL LYS SEQRES 17 A 552 THR TYR LEU SER ASN GLU TYR SER LYS GLU ILE ASP GLU SEQRES 18 A 552 LEU ASN THR TYR ILE GLU GLU SER LEU ASN LYS ILE THR SEQRES 19 A 552 GLN ASN SER GLY ASN ASP VAL ARG ASN PHE GLU GLU PHE SEQRES 20 A 552 LYS ASN GLY GLU SER PHE ASN LEU TYR GLU GLN GLU LEU SEQRES 21 A 552 VAL GLU ARG TRP ASN LEU ALA ALA ALA SER ASP ILE LEU SEQRES 22 A 552 ARG ILE SER ALA LEU LYS GLU ILE GLY GLY MET TYR LEU SEQRES 23 A 552 ASP VAL ASP MET LEU PRO GLY ILE GLN PRO ASP LEU PHE SEQRES 24 A 552 GLU SER ILE GLU LYS PRO SER SER VAL THR VAL ASP PHE SEQRES 25 A 552 TRP GLU MET THR LYS LEU GLU ALA ILE MET LYS TYR LYS SEQRES 26 A 552 GLU TYR ILE PRO GLU TYR THR SER GLU HIS PHE ASP MET SEQRES 27 A 552 LEU ASP GLU GLU VAL GLN SER SER PHE GLU SER VAL LEU SEQRES 28 A 552 ALA SER LYS SER ASP LYS SER GLU ILE PHE SER SER LEU SEQRES 29 A 552 GLY ASP MET GLU ALA SER PRO LEU GLU VAL LYS ILE ALA SEQRES 30 A 552 PHE ASN SER LYS GLY ILE ILE ASN GLN GLY LEU ILE SER SEQRES 31 A 552 VAL LYS ASP SER TYR CYS SER ASN LEU ILE VAL LYS GLN SEQRES 32 A 552 ILE GLU ASN ARG TYR LYS ILE LEU ASN ASN SER LEU ASN SEQRES 33 A 552 PRO ALA ILE SER GLU ASP ASN ASP PHE ASN THR THR THR SEQRES 34 A 552 ASN THR PHE ILE ASP SER ILE MET ALA GLU ALA ASN ALA SEQRES 35 A 552 ASP ASN GLY ARG PHE MET MET GLU LEU GLY LYS TYR LEU SEQRES 36 A 552 ARG VAL GLY PHE PHE PRO ASP VAL LYS THR THR ILE ASN SEQRES 37 A 552 LEU SER GLY PRO GLU ALA TYR ALA ALA ALA TYR GLN ASP SEQRES 38 A 552 LEU LEU MET PHE LYS GLU GLY SER MET ASN ILE HIS LEU SEQRES 39 A 552 ILE GLU ALA ASP LEU ARG ASN PHE GLU ILE SER LYS THR SEQRES 40 A 552 ASN ILE SER GLN SER THR GLU GLN GLU MET ALA SER LEU SEQRES 41 A 552 TRP SER PHE ASP ASP ALA ARG ALA LYS ALA GLN PHE GLU SEQRES 42 A 552 GLU TYR LYS ARG ASN TYR PHE GLU GLY SER LEU LEU GLU SEQRES 43 A 552 HIS HIS HIS HIS HIS HIS SEQRES 1 B 552 MET GLY SER LEU VAL ASN ARG LYS GLN LEU GLU LYS MET SEQRES 2 B 552 ALA ASN VAL ARG PHE ARG THR GLN GLU ASP GLU TYR VAL SEQRES 3 B 552 ALA ILE LEU ASP ALA LEU GLU GLU TYR HIS ASN MET SER SEQRES 4 B 552 GLU ASN THR VAL VAL GLU LYS TYR LEU LYS LEU LYS ASP SEQRES 5 B 552 ILE ASN SER LEU THR ASP ILE TYR ILE ASP THR TYR LYS SEQRES 6 B 552 LYS SER GLY ARG ASN LYS ALA LEU LYS LYS PHE LYS GLU SEQRES 7 B 552 TYR LEU VAL THR GLU VAL LEU GLU LEU LYS ASN ASN ASN SEQRES 8 B 552 LEU THR PRO VAL GLU LYS ASN LEU HIS PHE VAL TRP ILE SEQRES 9 B 552 GLY GLY GLN ILE ASN ASP THR ALA ILE ASN TYR ILE ASN SEQRES 10 B 552 GLN TRP LYS ASP VAL ASN SER ASP TYR ASN VAL ASN VAL SEQRES 11 B 552 PHE TYR ASP SER ASN ALA PHE LEU ILE ASN THR LEU LYS SEQRES 12 B 552 LYS THR VAL VAL GLU SER ALA ILE ASN ASP THR LEU GLU SEQRES 13 B 552 SER PHE ARG GLU ASN LEU ASN ASP PRO ARG PHE ASP TYR SEQRES 14 B 552 ASN LYS PHE PHE ARG LYS ARG MET GLU ILE ILE TYR ASP SEQRES 15 B 552 LYS GLN LYS ASN PHE ILE ASN TYR TYR LYS ALA GLN ARG SEQRES 16 B 552 GLU GLU ASN PRO GLU LEU ILE ILE ASP ASP ILE VAL LYS SEQRES 17 B 552 THR TYR LEU SER ASN GLU TYR SER LYS GLU ILE ASP GLU SEQRES 18 B 552 LEU ASN THR TYR ILE GLU GLU SER LEU ASN LYS ILE THR SEQRES 19 B 552 GLN ASN SER GLY ASN ASP VAL ARG ASN PHE GLU GLU PHE SEQRES 20 B 552 LYS ASN GLY GLU SER PHE ASN LEU TYR GLU GLN GLU LEU SEQRES 21 B 552 VAL GLU ARG TRP ASN LEU ALA ALA ALA SER ASP ILE LEU SEQRES 22 B 552 ARG ILE SER ALA LEU LYS GLU ILE GLY GLY MET TYR LEU SEQRES 23 B 552 ASP VAL ASP MET LEU PRO GLY ILE GLN PRO ASP LEU PHE SEQRES 24 B 552 GLU SER ILE GLU LYS PRO SER SER VAL THR VAL ASP PHE SEQRES 25 B 552 TRP GLU MET THR LYS LEU GLU ALA ILE MET LYS TYR LYS SEQRES 26 B 552 GLU TYR ILE PRO GLU TYR THR SER GLU HIS PHE ASP MET SEQRES 27 B 552 LEU ASP GLU GLU VAL GLN SER SER PHE GLU SER VAL LEU SEQRES 28 B 552 ALA SER LYS SER ASP LYS SER GLU ILE PHE SER SER LEU SEQRES 29 B 552 GLY ASP MET GLU ALA SER PRO LEU GLU VAL LYS ILE ALA SEQRES 30 B 552 PHE ASN SER LYS GLY ILE ILE ASN GLN GLY LEU ILE SER SEQRES 31 B 552 VAL LYS ASP SER TYR CYS SER ASN LEU ILE VAL LYS GLN SEQRES 32 B 552 ILE GLU ASN ARG TYR LYS ILE LEU ASN ASN SER LEU ASN SEQRES 33 B 552 PRO ALA ILE SER GLU ASP ASN ASP PHE ASN THR THR THR SEQRES 34 B 552 ASN THR PHE ILE ASP SER ILE MET ALA GLU ALA ASN ALA SEQRES 35 B 552 ASP ASN GLY ARG PHE MET MET GLU LEU GLY LYS TYR LEU SEQRES 36 B 552 ARG VAL GLY PHE PHE PRO ASP VAL LYS THR THR ILE ASN SEQRES 37 B 552 LEU SER GLY PRO GLU ALA TYR ALA ALA ALA TYR GLN ASP SEQRES 38 B 552 LEU LEU MET PHE LYS GLU GLY SER MET ASN ILE HIS LEU SEQRES 39 B 552 ILE GLU ALA ASP LEU ARG ASN PHE GLU ILE SER LYS THR SEQRES 40 B 552 ASN ILE SER GLN SER THR GLU GLN GLU MET ALA SER LEU SEQRES 41 B 552 TRP SER PHE ASP ASP ALA ARG ALA LYS ALA GLN PHE GLU SEQRES 42 B 552 GLU TYR LYS ARG ASN TYR PHE GLU GLY SER LEU LEU GLU SEQRES 43 B 552 HIS HIS HIS HIS HIS HIS HET NOY A 601 11 HET UDP A 602 25 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET MN A 606 1 HET NOY B 601 11 HET UDP B 602 25 HET GOL B 603 6 HET GOL B 604 6 HET MN B 605 1 HETNAM NOY (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM MN MANGANESE (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NOY 2(C6 H13 N O4) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 5 GOL 5(C3 H8 O3) FORMUL 8 MN 2(MN 2+) FORMUL 14 HOH *223(H2 O) HELIX 1 AA1 ASN A 5 ALA A 13 1 9 HELIX 2 AA2 GLU A 21 HIS A 35 1 15 HELIX 3 AA3 THR A 41 TYR A 63 1 23 HELIX 4 AA4 ARG A 68 ASN A 90 1 23 HELIX 5 AA5 ASN A 108 ASN A 122 1 15 HELIX 6 AA6 LEU A 137 SER A 156 1 20 HELIX 7 AA7 PHE A 157 ASN A 162 5 6 HELIX 8 AA8 ASP A 167 ASN A 197 1 31 HELIX 9 AA9 ILE A 201 SER A 215 1 15 HELIX 10 AB1 GLU A 217 GLN A 234 1 18 HELIX 11 AB2 PHE A 243 GLY A 249 1 7 HELIX 12 AB3 SER A 251 GLU A 261 1 11 HELIX 13 AB4 ASN A 264 GLY A 281 1 18 HELIX 14 AB5 THR A 308 GLU A 325 1 18 HELIX 15 AB6 HIS A 334 LEU A 338 5 5 HELIX 16 AB7 ASP A 339 SER A 352 1 14 HELIX 17 AB8 ASP A 355 ILE A 359 5 5 HELIX 18 AB9 SER A 393 GLU A 420 1 28 HELIX 19 AC1 ASP A 423 ALA A 439 1 17 HELIX 20 AC2 ASN A 443 MET A 448 1 6 HELIX 21 AC3 LYS A 452 VAL A 456 5 5 HELIX 22 AC4 THR A 464 SER A 469 1 6 HELIX 23 AC5 GLY A 470 MET A 483 1 14 HELIX 24 AC6 ILE A 494 ARG A 499 1 6 HELIX 25 AC7 ASN A 500 GLU A 502 5 3 HELIX 26 AC8 SER A 504 THR A 506 5 3 HELIX 27 AC9 GLU A 513 ALA A 517 5 5 HELIX 28 AD1 ASP A 523 PHE A 539 1 17 HELIX 29 AD2 ASN B 5 ALA B 13 1 9 HELIX 30 AD3 GLU B 21 HIS B 35 1 15 HELIX 31 AD4 THR B 41 TYR B 63 1 23 HELIX 32 AD5 ARG B 68 ASN B 90 1 23 HELIX 33 AD6 ASN B 108 ASN B 122 1 15 HELIX 34 AD7 LEU B 137 PHE B 157 1 21 HELIX 35 AD8 ARG B 158 ASN B 162 5 5 HELIX 36 AD9 ASP B 167 ASN B 197 1 31 HELIX 37 AE1 ILE B 201 SER B 215 1 15 HELIX 38 AE2 GLU B 217 GLN B 234 1 18 HELIX 39 AE3 PHE B 243 ASN B 248 1 6 HELIX 40 AE4 SER B 251 GLU B 261 1 11 HELIX 41 AE5 ASN B 264 GLY B 281 1 18 HELIX 42 AE6 THR B 308 GLU B 325 1 18 HELIX 43 AE7 HIS B 334 LEU B 338 5 5 HELIX 44 AE8 ASP B 339 SER B 352 1 14 HELIX 45 AE9 ASP B 355 ILE B 359 5 5 HELIX 46 AF1 SER B 393 GLU B 420 1 28 HELIX 47 AF2 ASP B 423 ALA B 439 1 17 HELIX 48 AF3 ASN B 443 GLY B 451 1 9 HELIX 49 AF4 LYS B 452 VAL B 456 5 5 HELIX 50 AF5 THR B 464 SER B 469 1 6 HELIX 51 AF6 GLY B 470 MET B 483 1 14 HELIX 52 AF7 ILE B 494 ARG B 499 1 6 HELIX 53 AF8 ASN B 500 GLU B 502 5 3 HELIX 54 AF9 SER B 504 THR B 506 5 3 HELIX 55 AG1 GLU B 513 ALA B 517 5 5 HELIX 56 AG2 ASP B 523 PHE B 539 1 17 SHEET 1 AA1 2 THR A 92 PRO A 93 0 SHEET 2 AA1 2 GLU A 367 ALA A 368 -1 O ALA A 368 N THR A 92 SHEET 1 AA2 6 GLY A 237 ASP A 239 0 SHEET 2 AA2 6 ASN A 126 TYR A 131 1 N TYR A 131 O ASN A 238 SHEET 3 AA2 6 ASN A 97 VAL A 101 1 N PHE A 100 O PHE A 130 SHEET 4 AA2 6 GLY A 282 LEU A 285 1 O MET A 283 N HIS A 99 SHEET 5 AA2 6 GLY A 381 SER A 389 -1 O SER A 389 N GLY A 282 SHEET 6 AA2 6 LYS A 374 ASN A 378 -1 N LYS A 374 O ILE A 388 SHEET 1 AA3 2 LEU A 290 PRO A 291 0 SHEET 2 AA3 2 ILE A 508 SER A 509 -1 O SER A 509 N LEU A 290 SHEET 1 AA4 2 THR B 92 PRO B 93 0 SHEET 2 AA4 2 GLU B 367 ALA B 368 -1 O ALA B 368 N THR B 92 SHEET 1 AA5 6 GLY B 237 ASP B 239 0 SHEET 2 AA5 6 ASN B 126 TYR B 131 1 N TYR B 131 O ASN B 238 SHEET 3 AA5 6 ASN B 97 VAL B 101 1 N PHE B 100 O PHE B 130 SHEET 4 AA5 6 GLY B 282 LEU B 285 1 O MET B 283 N HIS B 99 SHEET 5 AA5 6 GLY B 381 SER B 389 -1 O SER B 389 N GLY B 282 SHEET 6 AA5 6 LYS B 374 ASN B 378 -1 N LYS B 374 O ILE B 388 SHEET 1 AA6 2 LEU B 290 PRO B 291 0 SHEET 2 AA6 2 ILE B 508 SER B 509 -1 O SER B 509 N LEU B 290 LINK OD2 ASP A 288 MN MN A 606 1555 1555 2.08 LINK OE1 GLU A 515 MN MN A 606 1555 1555 2.21 LINK O1A UDP A 602 MN MN A 606 1555 1555 2.20 LINK O2B UDP A 602 MN MN A 606 1555 1555 1.92 LINK MN MN A 606 O HOH A 708 1555 1555 2.08 LINK MN MN A 606 O HOH A 733 1555 1555 2.33 LINK OD2 ASP B 288 MN MN B 605 1555 1555 2.00 LINK OE1 GLU B 515 MN MN B 605 1555 1555 2.13 LINK O1A UDP B 602 MN MN B 605 1555 1555 2.24 LINK O3B UDP B 602 MN MN B 605 1555 1555 2.18 LINK MN MN B 605 O HOH B 709 1555 1555 2.19 LINK MN MN B 605 O HOH B 718 1555 1555 2.23 CRYST1 152.589 82.676 113.227 90.00 92.43 90.00 C 1 2 1 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 0.006554 0.000000 0.000278 0.00000 SCALE2 0.000000 0.012095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008840 0.00000