HEADER TRANSFERASE 17-AUG-17 5Y7F TITLE CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF UGGT (UDP-BOUND FORM) FROM TITLE 2 THERMOMYCES DUPONTII COMPND MOL_ID: 1; COMPND 2 MOLECULE: UGGT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOMYCES DUPONTII; SOURCE 3 ORGANISM_TAXID: 28565; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOLD-I KEYWDS ENDOPLASMIC RETICULUM, QUALITY CONTROL, GLUCOSYLTRANSFERASE, FOLDING KEYWDS 2 SENSOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,C.SONG,T.ZHU,T.TOSHIMORI,K.MURATA,Y.HAYASHI,H.KAMIKUBO, AUTHOR 2 T.UCHIHASHI,K.KATO REVDAT 3 22-NOV-23 5Y7F 1 REMARK REVDAT 2 01-NOV-17 5Y7F 1 JRNL REVDAT 1 27-SEP-17 5Y7F 0 JRNL AUTH T.SATOH,C.SONG,T.ZHU,T.TOSHIMORI,K.MURATA,Y.HAYASHI, JRNL AUTH 2 H.KAMIKUBO,T.UCHIHASHI,K.KATO JRNL TITL VISUALISATION OF A FLEXIBLE MODULAR STRUCTURE OF THE ER JRNL TITL 2 FOLDING-SENSOR ENZYME UGGT. JRNL REF SCI REP V. 7 12142 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28939828 JRNL DOI 10.1038/S41598-017-12283-W REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 59135 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3112 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3887 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 204 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : 0.75000 REMARK 3 B33 (A**2) : -0.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.039 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.155 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2340 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2139 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3173 ; 1.671 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4949 ; 0.956 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 265 ; 6.234 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 117 ;36.604 ;23.162 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;14.002 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.919 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2529 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 521 ; 0.002 ; 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): 1067 ; 1.284 ; 1.344 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1065 ; 1.280 ; 1.342 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1329 ; 1.468 ; 2.019 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1330 ; 1.467 ; 2.020 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1273 ; 1.818 ; 1.628 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1273 ; 1.817 ; 1.628 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1845 ; 2.056 ; 2.338 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2757 ; 2.308 ;16.643 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2718 ; 2.232 ;16.378 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4479 ; 1.991 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 148 ;16.465 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4485 ; 4.954 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 REMARK 4 REMARK 4 5Y7F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004800. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62275 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.79600 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: MOLREP REMARK 200 STARTING MODEL: 5H18 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION BUFFER 24% PEG 3350, REMARK 280 100 MM TRIS-HCL (PH 9.0), SOAKING BUFFER 24% PEG 3350, 100 MM REMARK 280 TRIS-HCL (PH 9.0), 2 MM CACL2, 10 MM UDP, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.70500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.99500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.99500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.42500 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 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 GLY A 1188 REMARK 465 SER A 1189 REMARK 465 SER A 1378 REMARK 465 ALA A 1379 REMARK 465 ASP A 1380 REMARK 465 PRO A 1381 REMARK 465 ASN A 1382 REMARK 465 SER A 1383 REMARK 465 VAL A 1463 REMARK 465 ARG A 1464 REMARK 465 ALA A 1465 REMARK 465 ALA A 1466 REMARK 465 SER A 1467 REMARK 465 LYS A 1468 REMARK 465 GLN A 1469 REMARK 465 SER A 1470 REMARK 465 ARG A 1471 REMARK 465 ARG A 1472 REMARK 465 GLU A 1473 REMARK 465 GLU A 1474 REMARK 465 ASP A 1475 REMARK 465 GLU A 1476 REMARK 465 LYS A 1477 REMARK 465 LYS A 1478 REMARK 465 ASP A 1479 REMARK 465 VAL A 1480 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 NH2 ARG A 1362 O HOH A 2101 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MSE A1211 CG - SE - CE ANGL. DEV. = -16.4 DEGREES REMARK 500 ASP A1357 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES 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 ASP A1296 45.38 -89.63 REMARK 500 LEU A1428 39.69 -93.03 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 CA A2003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1294 OD2 REMARK 620 2 ASP A1296 OD1 94.8 REMARK 620 3 ASP A1296 OD2 147.8 53.5 REMARK 620 4 ASP A1427 OD1 88.7 81.6 91.7 REMARK 620 5 ASP A1427 OD2 109.9 124.1 95.1 51.2 REMARK 620 6 UDP A2001 O2A 86.9 76.1 80.2 156.8 150.6 REMARK 620 7 UDP A2001 O2B 97.6 148.2 107.4 127.7 78.4 75.5 REMARK 620 N 1 2 3 4 5 6 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 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 2003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H18 RELATED DB: PDB DBREF 5Y7F A 1188 1480 PDB 5Y7F 5Y7F 1188 1480 SEQRES 1 A 293 GLY SER ALA ASP ILE ASN ILE PHE SER VAL ALA SER GLY SEQRES 2 A 293 HIS LEU TYR GLU ARG MSE LEU ASN ILE MSE MSE VAL SER SEQRES 3 A 293 VAL MSE LYS HIS THR LYS HIS SER VAL LYS PHE TRP PHE SEQRES 4 A 293 ILE GLU GLN PHE LEU SER PRO SER PHE LYS LYS PHE LEU SEQRES 5 A 293 PRO HIS LEU ALA LYS GLU TYR GLY PHE SER TYR GLU MSE SEQRES 6 A 293 VAL THR TYR LYS TRP PRO HIS TRP LEU ARG GLY GLN ARG SEQRES 7 A 293 GLU LYS GLN ARG GLU ILE TRP GLY TYR LYS ILE LEU PHE SEQRES 8 A 293 LEU ASP VAL LEU PHE PRO LEU SER LEU ASP LYS VAL ILE SEQRES 9 A 293 PHE VAL ASP ALA ASP GLN ILE VAL ARG THR ASP MSE TYR SEQRES 10 A 293 ASP LEU VAL GLN LEU ASP LEU GLU GLY ALA PRO TYR GLY SEQRES 11 A 293 PHE THR PRO MSE CYS ASP SER ARG LYS GLU MSE GLU GLY SEQRES 12 A 293 PHE ARG PHE TRP LYS GLN GLY TYR TRP LYS SER HIS LEU SEQRES 13 A 293 ARG GLY ARG PRO TYR HIS ILE SER ALA LEU TYR VAL VAL SEQRES 14 A 293 ASP LEU ASN ARG PHE ARG ALA LEU ALA ALA GLY ASP ARG SEQRES 15 A 293 LEU ARG GLY GLN TYR HIS THR LEU SER ALA ASP PRO ASN SEQRES 16 A 293 SER LEU ALA ASN LEU ASP GLN ASP LEU PRO ASN ASN MSE SEQRES 17 A 293 GLN ALA MSE ILE PRO ILE LYS SER LEU PRO GLN GLU TRP SEQRES 18 A 293 LEU TRP CYS GLU THR TRP CYS ALA ASP GLU ASP LEU LYS SEQRES 19 A 293 THR ALA ARG THR ILE ASP LEU CYS ASN ASN PRO LEU THR SEQRES 20 A 293 LYS GLU PRO LYS LEU ASP ARG ALA ARG ARG GLN VAL PRO SEQRES 21 A 293 GLU TRP THR GLU TYR ASP ASN GLU ILE ALA GLU LEU ALA SEQRES 22 A 293 VAL ARG VAL ARG ALA ALA SER LYS GLN SER ARG ARG GLU SEQRES 23 A 293 GLU ASP GLU LYS LYS ASP VAL HET MSE A1206 8 HET MSE A1210 8 HET MSE A1211 8 HET MSE A1215 8 HET MSE A1252 8 HET MSE A1303 8 HET MSE A1321 8 HET MSE A1328 8 HET MSE A1395 8 HET MSE A1398 8 HET UDP A2001 25 HET TRS A2002 8 HET CA A2003 1 HETNAM MSE SELENOMETHIONINE HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CA CALCIUM ION HETSYN TRS TRIS BUFFER FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 2 UDP C9 H14 N2 O12 P2 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 CA CA 2+ FORMUL 5 HOH *220(H2 O) HELIX 1 AA1 GLY A 1200 HIS A 1217 1 18 HELIX 2 AA2 GLN A 1229 LEU A 1231 5 3 HELIX 3 AA3 SER A 1232 GLY A 1247 1 16 HELIX 4 AA4 GLU A 1266 LEU A 1277 1 12 HELIX 5 AA5 MSE A 1303 LEU A 1309 1 7 HELIX 6 AA6 ARG A 1325 LYS A 1335 5 11 HELIX 7 AA7 GLN A 1336 ARG A 1344 1 9 HELIX 8 AA8 LEU A 1358 LEU A 1364 1 7 HELIX 9 AA9 ALA A 1365 LEU A 1377 1 13 HELIX 10 AB1 ASN A 1386 MSE A 1395 1 10 HELIX 11 AB2 PRO A 1405 LEU A 1409 5 5 HELIX 12 AB3 ALA A 1416 ALA A 1423 5 8 HELIX 13 AB4 PRO A 1437 VAL A 1446 1 10 HELIX 14 AB5 PRO A 1447 ARG A 1462 1 16 SHEET 1 AA1 7 SER A1249 VAL A1253 0 SHEET 2 AA1 7 VAL A1222 ILE A1227 1 N PHE A1224 O SER A1249 SHEET 3 AA1 7 ILE A1192 PHE A1195 1 N ILE A1192 O LYS A1223 SHEET 4 AA1 7 LYS A1289 VAL A1293 1 O ILE A1291 N PHE A1195 SHEET 5 AA1 7 HIS A1349 ASP A1357 -1 O VAL A1356 N VAL A1290 SHEET 6 AA1 7 TYR A1316 PRO A1320 -1 N THR A1319 O ILE A1350 SHEET 7 AA1 7 ILE A1401 SER A1403 1 O LYS A1402 N TYR A1316 SHEET 1 AA2 2 GLN A1297 VAL A1299 0 SHEET 2 AA2 2 THR A1425 ASP A1427 -1 O ILE A1426 N ILE A1298 SSBOND 1 CYS A 1322 CYS A 1415 1555 1555 2.04 SSBOND 2 CYS A 1411 CYS A 1429 1555 1555 2.04 LINK C ARG A1205 N MSE A1206 1555 1555 1.32 LINK C MSE A1206 N LEU A1207 1555 1555 1.33 LINK C ILE A1209 N MSE A1210 1555 1555 1.33 LINK C MSE A1210 N MSE A1211 1555 1555 1.31 LINK C MSE A1211 N VAL A1212 1555 1555 1.33 LINK C VAL A1214 N MSE A1215 1555 1555 1.33 LINK C MSE A1215 N LYS A1216 1555 1555 1.33 LINK C GLU A1251 N MSE A1252 1555 1555 1.32 LINK C MSE A1252 N VAL A1253 1555 1555 1.32 LINK C ASP A1302 N MSE A1303 1555 1555 1.32 LINK C MSE A1303 N TYR A1304 1555 1555 1.34 LINK C PRO A1320 N MSE A1321 1555 1555 1.32 LINK C MSE A1321 N CYS A1322 1555 1555 1.33 LINK C GLU A1327 N MSE A1328 1555 1555 1.34 LINK C MSE A1328 N GLU A1329 1555 1555 1.33 LINK C ASN A1394 N MSE A1395 1555 1555 1.33 LINK C MSE A1395 N GLN A1396 1555 1555 1.32 LINK C ALA A1397 N MSE A1398 1555 1555 1.33 LINK C MSE A1398 N ILE A1399 1555 1555 1.34 LINK OD2 ASP A1294 CA CA A2003 1555 1555 2.29 LINK OD1 ASP A1296 CA CA A2003 1555 1555 2.30 LINK OD2 ASP A1296 CA CA A2003 1555 1555 2.52 LINK OD1 ASP A1427 CA CA A2003 1555 1555 2.39 LINK OD2 ASP A1427 CA CA A2003 1555 1555 2.53 LINK O2A UDP A2001 CA CA A2003 1555 1555 2.48 LINK O2B UDP A2001 CA CA A2003 1555 1555 2.44 SITE 1 AC1 20 VAL A1197 ALA A1198 SER A1199 TYR A1203 SITE 2 AC1 20 ILE A1271 TRP A1272 ASP A1294 ALA A1295 SITE 3 AC1 20 ASP A1296 ASP A1427 CYS A1429 ASN A1430 SITE 4 AC1 20 LYS A1438 ARG A1462 TRS A2002 CA A2003 SITE 5 AC1 20 HOH A2119 HOH A2151 HOH A2172 HOH A2219 SITE 1 AC2 8 TRP A1272 ASN A1386 LEU A1387 ASP A1388 SITE 2 AC2 8 GLN A1389 UDP A2001 HOH A2152 HOH A2211 SITE 1 AC3 4 ASP A1294 ASP A1296 ASP A1427 UDP A2001 CRYST1 45.410 46.850 131.990 90.00 90.00 90.00 P 21 21 21 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 0.022022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007576 0.00000