HEADER TRANSFERASE 15-JAN-13 4IRP TITLE CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1,4- TITLE 2 GALACTOSYLTRANSFERASE-7 IN OPEN CONFORMATION WITH MANGANSES AND UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-1,4-GALACTOSYLTRANSFERASE 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA-1,4-GALTASE 7, BETA4GAL-T7, B4GAL-T7, UDP-GAL:BETA- COMPND 5 GLCNAC BETA-1,4-GALACTOSYLTRANSFERASE 7, UDP-GALACTOSE:BETA-N- COMPND 6 ACETYLGLUCOSAMINE BETA-1,4-GALACTOSYLTRANSFERASE 7, XYLOSYLPROTEIN 4- COMPND 7 BETA-GALACTOSYLTRANSFERASE, PROTEOGLYCAN UDP-GALACTOSE:BETA-XYLOSE COMPND 8 BETA1,4-GALACTOSYLTRANSFERASE I, UDP-GALACTOSE:BETA-XYLOSE BETA-1,4- COMPND 9 GALACTOSYLTRANSFERASE, XGPT, XGALT-1, XYLOSYLPROTEIN BETA-1,4- COMPND 10 GALACTOSYLTRANSFERASE; COMPND 11 EC: 2.4.1.-, 2.4.1.133; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: 4GALACTOSYLTRANSFERASE, B4GALT7, BETA1, UNQ748/PRO1478, SOURCE 6 XGALT1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS GT-A FOLD, OPEN CONFORMATION, MANGANESE AND UDP COMPLEX, KEYWDS 2 GLYCOSYLTRANSFERASE, GOLGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TSUTSUI,B.RAMAKRISHNAN,P.K.QASBA REVDAT 3 20-SEP-23 4IRP 1 REMARK SEQADV LINK REVDAT 2 27-NOV-13 4IRP 1 JRNL REVDAT 1 25-SEP-13 4IRP 0 JRNL AUTH Y.TSUTSUI,B.RAMAKRISHNAN,P.K.QASBA JRNL TITL CRYSTAL STRUCTURES OF BETA-1,4-GALACTOSYLTRANSFERASE 7 JRNL TITL 2 ENZYME REVEAL CONFORMATIONAL CHANGES AND SUBSTRATE BINDING. JRNL REF J.BIOL.CHEM. V. 288 31963 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24052259 JRNL DOI 10.1074/JBC.M113.509984 REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 40726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2081 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 44.2697 - 5.1766 0.98 2761 125 0.2825 0.3358 REMARK 3 2 5.1766 - 4.1097 0.99 2645 139 0.1981 0.2630 REMARK 3 3 4.1097 - 3.5905 0.99 2598 142 0.1940 0.2304 REMARK 3 4 3.5905 - 3.2623 0.99 2592 141 0.2027 0.2580 REMARK 3 5 3.2623 - 3.0286 0.99 2596 123 0.2162 0.2598 REMARK 3 6 3.0286 - 2.8500 1.00 2538 161 0.2232 0.2773 REMARK 3 7 2.8500 - 2.7073 0.99 2579 133 0.2111 0.2637 REMARK 3 8 2.7073 - 2.5895 1.00 2562 125 0.2201 0.2706 REMARK 3 9 2.5895 - 2.4898 1.00 2566 143 0.2175 0.3300 REMARK 3 10 2.4898 - 2.4039 1.00 2550 132 0.2080 0.2674 REMARK 3 11 2.4039 - 2.3287 0.99 2556 128 0.2087 0.2842 REMARK 3 12 2.3287 - 2.2622 0.99 2532 145 0.2102 0.3076 REMARK 3 13 2.2622 - 2.2026 0.99 2539 137 0.2103 0.2814 REMARK 3 14 2.2026 - 2.1489 0.99 2526 145 0.2300 0.2810 REMARK 3 15 2.1489 - 2.1000 0.99 2505 162 0.2383 0.3053 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.550 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 : 0.022 4144 REMARK 3 ANGLE : 1.930 5647 REMARK 3 CHIRALITY : 0.139 577 REMARK 3 PLANARITY : 0.010 730 REMARK 3 DIHEDRAL : 15.388 1541 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 4IRP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 36.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3LW6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 TO 1.0 M SODIUM ACCETATE, 100 MM REMARK 280 IMIDAZOLE.HCL PH 6.5 AS PRECIPATING AGENT, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 43.66300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.59300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.59300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.83150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.59300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.59300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.49450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.59300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.59300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.83150 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.59300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.59300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.49450 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 43.66300 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 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: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 260 REMARK 465 PRO A 261 REMARK 465 ALA A 262 REMARK 465 TRP A 263 REMARK 465 ARG A 264 REMARK 465 LYS A 265 REMARK 465 ARG A 266 REMARK 465 ASP A 267 REMARK 465 GLN A 268 REMARK 465 LYS A 269 REMARK 465 ARG A 270 REMARK 465 ILE A 271 REMARK 465 ALA A 272 REMARK 465 ALA A 273 REMARK 465 GLN A 274 REMARK 465 LYS A 275 REMARK 465 GLN A 276 REMARK 465 GLU A 277 REMARK 465 GLN A 278 REMARK 465 HIS B 259 REMARK 465 ASP B 260 REMARK 465 PRO B 261 REMARK 465 ALA B 262 REMARK 465 TRP B 263 REMARK 465 ARG B 264 REMARK 465 LYS B 265 REMARK 465 ARG B 266 REMARK 465 ASP B 267 REMARK 465 GLN B 268 REMARK 465 LYS B 269 REMARK 465 ARG B 270 REMARK 465 ILE B 271 REMARK 465 ALA B 272 REMARK 465 ALA B 273 REMARK 465 GLN B 274 REMARK 465 LYS B 275 REMARK 465 GLN B 276 REMARK 465 GLU B 277 REMARK 465 GLN B 278 REMARK 465 PHE B 279 REMARK 465 LYS B 280 REMARK 465 VAL B 281 REMARK 465 ASP B 282 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 PRO A 92 C - N - CA ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG B 116 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 116 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP B 174 CB - CG - OD1 ANGL. DEV. = 6.0 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 LEU A 193 -71.09 -127.86 REMARK 500 HIS A 195 19.90 -141.23 REMARK 500 GLU B 103 62.40 37.75 REMARK 500 ASN B 140 79.40 -117.46 REMARK 500 ALA B 186 55.19 -90.98 REMARK 500 LEU B 193 -63.15 -129.89 REMARK 500 TRP B 323 0.60 -65.16 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 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 257 NE2 REMARK 620 2 UDP A 401 O1A 163.5 REMARK 620 3 HOH A 653 O 111.6 83.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 165 OD2 REMARK 620 2 HIS B 257 NE2 100.7 REMARK 620 3 UDP B 401 O1B 139.5 118.9 REMARK 620 4 UDP B 401 O1A 68.6 167.2 71.0 REMARK 620 5 HOH B 636 O 96.4 106.5 81.0 82.3 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 UDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IRQ RELATED DB: PDB DBREF 4IRP A 81 327 UNP Q9UBV7 B4GT7_HUMAN 81 327 DBREF 4IRP B 81 327 UNP Q9UBV7 B4GT7_HUMAN 81 327 SEQADV 4IRP GLY A 77 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP SER A 78 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP ASP A 79 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP ILE A 80 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP GLY B 77 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP SER B 78 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP ASP B 79 UNP Q9UBV7 EXPRESSION TAG SEQADV 4IRP ILE B 80 UNP Q9UBV7 EXPRESSION TAG SEQRES 1 A 251 GLY SER ASP ILE PRO GLU HIS TRP GLU GLU ASP ALA SER SEQRES 2 A 251 TRP GLY PRO HIS ARG LEU ALA VAL LEU VAL PRO PHE ARG SEQRES 3 A 251 GLU ARG PHE GLU GLU LEU LEU VAL PHE VAL PRO HIS MET SEQRES 4 A 251 ARG ARG PHE LEU SER ARG LYS LYS ILE ARG HIS HIS ILE SEQRES 5 A 251 TYR VAL LEU ASN GLN VAL ASP HIS PHE ARG PHE ASN ARG SEQRES 6 A 251 ALA ALA LEU ILE ASN VAL GLY PHE LEU GLU SER SER ASN SEQRES 7 A 251 SER THR ASP TYR ILE ALA MET HIS ASP VAL ASP LEU LEU SEQRES 8 A 251 PRO LEU ASN GLU GLU LEU ASP TYR GLY PHE PRO GLU ALA SEQRES 9 A 251 GLY PRO PHE HIS VAL ALA SER PRO GLU LEU HIS PRO LEU SEQRES 10 A 251 TYR HIS TYR LYS THR TYR VAL GLY GLY ILE LEU LEU LEU SEQRES 11 A 251 SER LYS GLN HIS TYR ARG LEU CYS ASN GLY MET SER ASN SEQRES 12 A 251 ARG PHE TRP GLY TRP GLY ARG GLU ASP ASP GLU PHE TYR SEQRES 13 A 251 ARG ARG ILE LYS GLY ALA GLY LEU GLN LEU PHE ARG PRO SEQRES 14 A 251 SER GLY ILE THR THR GLY TYR LYS THR PHE ARG HIS LEU SEQRES 15 A 251 HIS ASP PRO ALA TRP ARG LYS ARG ASP GLN LYS ARG ILE SEQRES 16 A 251 ALA ALA GLN LYS GLN GLU GLN PHE LYS VAL ASP ARG GLU SEQRES 17 A 251 GLY GLY LEU ASN THR VAL LYS TYR HIS VAL ALA SER ARG SEQRES 18 A 251 THR ALA LEU SER VAL GLY GLY ALA PRO CYS THR VAL LEU SEQRES 19 A 251 ASN ILE MET LEU ASP CYS ASP LYS THR ALA THR PRO TRP SEQRES 20 A 251 CYS THR PHE SER SEQRES 1 B 251 GLY SER ASP ILE PRO GLU HIS TRP GLU GLU ASP ALA SER SEQRES 2 B 251 TRP GLY PRO HIS ARG LEU ALA VAL LEU VAL PRO PHE ARG SEQRES 3 B 251 GLU ARG PHE GLU GLU LEU LEU VAL PHE VAL PRO HIS MET SEQRES 4 B 251 ARG ARG PHE LEU SER ARG LYS LYS ILE ARG HIS HIS ILE SEQRES 5 B 251 TYR VAL LEU ASN GLN VAL ASP HIS PHE ARG PHE ASN ARG SEQRES 6 B 251 ALA ALA LEU ILE ASN VAL GLY PHE LEU GLU SER SER ASN SEQRES 7 B 251 SER THR ASP TYR ILE ALA MET HIS ASP VAL ASP LEU LEU SEQRES 8 B 251 PRO LEU ASN GLU GLU LEU ASP TYR GLY PHE PRO GLU ALA SEQRES 9 B 251 GLY PRO PHE HIS VAL ALA SER PRO GLU LEU HIS PRO LEU SEQRES 10 B 251 TYR HIS TYR LYS THR TYR VAL GLY GLY ILE LEU LEU LEU SEQRES 11 B 251 SER LYS GLN HIS TYR ARG LEU CYS ASN GLY MET SER ASN SEQRES 12 B 251 ARG PHE TRP GLY TRP GLY ARG GLU ASP ASP GLU PHE TYR SEQRES 13 B 251 ARG ARG ILE LYS GLY ALA GLY LEU GLN LEU PHE ARG PRO SEQRES 14 B 251 SER GLY ILE THR THR GLY TYR LYS THR PHE ARG HIS LEU SEQRES 15 B 251 HIS ASP PRO ALA TRP ARG LYS ARG ASP GLN LYS ARG ILE SEQRES 16 B 251 ALA ALA GLN LYS GLN GLU GLN PHE LYS VAL ASP ARG GLU SEQRES 17 B 251 GLY GLY LEU ASN THR VAL LYS TYR HIS VAL ALA SER ARG SEQRES 18 B 251 THR ALA LEU SER VAL GLY GLY ALA PRO CYS THR VAL LEU SEQRES 19 B 251 ASN ILE MET LEU ASP CYS ASP LYS THR ALA THR PRO TRP SEQRES 20 B 251 CYS THR PHE SER HET UDP A 401 25 HET MN A 402 1 HET ACT A 403 4 HET ACT A 404 4 HET ACT A 405 4 HET ACT A 406 4 HET IMD A 407 5 HET UDP B 401 25 HET MN B 402 1 HET ACT B 403 4 HET ACT B 404 4 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM ACT ACETATE ION HETNAM IMD IMIDAZOLE FORMUL 3 UDP 2(C9 H14 N2 O12 P2) FORMUL 4 MN 2(MN 2+) FORMUL 5 ACT 6(C2 H3 O2 1-) FORMUL 9 IMD C3 H5 N2 1+ FORMUL 14 HOH *294(H2 O) HELIX 1 1 PRO A 81 GLU A 85 5 5 HELIX 2 2 ASP A 87 GLY A 91 5 5 HELIX 3 3 ARG A 104 LYS A 122 1 19 HELIX 4 4 ASN A 140 SER A 152 1 13 HELIX 5 5 LYS A 208 CYS A 214 1 7 HELIX 6 6 ARG A 226 ALA A 238 1 13 HELIX 7 7 THR A 321 PHE A 326 5 6 HELIX 8 8 PRO B 81 GLU B 85 5 5 HELIX 9 9 ASP B 87 GLY B 91 5 5 HELIX 10 10 ARG B 104 LYS B 122 1 19 HELIX 11 11 ASN B 140 SER B 152 1 13 HELIX 12 12 LYS B 208 CYS B 214 1 7 HELIX 13 13 ARG B 226 ALA B 238 1 13 HELIX 14 14 THR B 321 THR B 325 5 5 SHEET 1 A14 PHE A 183 HIS A 184 0 SHEET 2 A14 ILE A 203 SER A 207 -1 O LEU A 205 N PHE A 183 SHEET 3 A14 TYR A 158 HIS A 162 -1 N ILE A 159 O LEU A 206 SHEET 4 A14 LEU A 95 PHE A 101 1 N LEU A 98 O ALA A 160 SHEET 5 A14 HIS A 126 GLN A 133 1 O TYR A 129 N VAL A 99 SHEET 6 A14 ALA A 305 LEU A 314 1 O LEU A 310 N ASN A 132 SHEET 7 A14 TYR A 292 VAL A 302 -1 N LEU A 300 O CYS A 307 SHEET 8 A14 TYR B 292 VAL B 302 -1 O SER B 301 N SER A 301 SHEET 9 A14 ALA B 305 LEU B 314 -1 O VAL B 309 N THR B 298 SHEET 10 A14 ARG B 125 GLN B 133 1 N VAL B 130 O LEU B 310 SHEET 11 A14 ARG B 94 PHE B 101 1 N VAL B 99 O LEU B 131 SHEET 12 A14 TYR B 158 HIS B 162 1 O ALA B 160 N LEU B 98 SHEET 13 A14 ILE B 203 SER B 207 -1 O LEU B 206 N ILE B 159 SHEET 14 A14 PHE B 183 HIS B 184 -1 N PHE B 183 O LEU B 205 SHEET 1 B 2 LEU A 166 PRO A 168 0 SHEET 2 B 2 PHE A 255 HIS A 257 -1 O ARG A 256 N LEU A 167 SHEET 1 C 2 LEU B 166 PRO B 168 0 SHEET 2 C 2 PHE B 255 HIS B 257 -1 O ARG B 256 N LEU B 167 SSBOND 1 CYS A 316 CYS A 324 1555 1555 2.02 SSBOND 2 CYS B 316 CYS B 324 1555 1555 2.05 LINK NE2 HIS A 257 MN MN A 402 1555 1555 2.43 LINK O1A UDP A 401 MN MN A 402 1555 1555 2.58 LINK MN MN A 402 O HOH A 653 1555 1555 2.39 LINK OD2 ASP B 165 MN MN B 402 1555 1555 2.66 LINK NE2 HIS B 257 MN MN B 402 1555 1555 2.35 LINK O1B UDP B 401 MN MN B 402 1555 1555 2.37 LINK O1A UDP B 401 MN MN B 402 1555 1555 2.50 LINK MN MN B 402 O HOH B 636 1555 1555 2.47 SITE 1 AC1 12 PRO A 100 PHE A 101 ARG A 102 ARG A 104 SITE 2 AC1 12 PHE A 139 ASP A 163 VAL A 164 ASP A 165 SITE 3 AC1 12 TYR A 194 MN A 402 HOH A 579 HOH A 617 SITE 1 AC2 4 ASP A 165 HIS A 257 UDP A 401 HOH A 653 SITE 1 AC3 3 ARG A 138 PHE A 139 GLY A 223 SITE 1 AC4 4 ASP A 79 PRO A 81 ARG A 117 ARG A 297 SITE 1 AC5 7 GLY A 91 PRO A 92 HOH A 650 ALA B 88 SITE 2 AC5 7 GLY B 91 PRO B 92 HOH B 637 SITE 1 AC6 3 ASP A 174 GLY A 176 PHE A 177 SITE 1 AC7 4 PHE A 243 HOH A 605 HOH A 608 HOH B 578 SITE 1 AC8 11 PRO B 100 PHE B 101 ARG B 102 ARG B 104 SITE 2 AC8 11 PHE B 139 ASP B 163 VAL B 164 ASP B 165 SITE 3 AC8 11 TYR B 194 MN B 402 HOH B 501 SITE 1 AC9 4 ASP B 165 HIS B 257 UDP B 401 HOH B 636 SITE 1 BC1 2 PRO B 92 SER B 155 SITE 1 BC2 2 TRP B 84 GLU B 85 CRYST1 125.186 125.186 87.326 90.00 90.00 90.00 P 41 21 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 0.007988 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011451 0.00000