HEADER TRANSFERASE 21-APR-11 3RMW TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) T83M MUTANT COMPLEXED TITLE 2 WITH MANGANESE AND UDP-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGENIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-262; COMPND 5 SYNONYM: GN-1, GN1; COMPND 6 EC: 2.4.1.186; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GYG, GYG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 TRANSFERASE, GLYCOSYLTRANSFERASE, GLYCOGEN BIOSYNTHESIS, KEYWDS 3 GLYCOSYLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.CHAIKUAD,D.S.FROESE,W.W.YUE,E.KRYSZTOFINSKA,F.VON DELFT,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,U.OPPERMANN,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 5 13-SEP-23 3RMW 1 REMARK SEQADV LINK REVDAT 4 11-JAN-12 3RMW 1 JRNL REVDAT 3 28-DEC-11 3RMW 1 JRNL REVDAT 2 14-DEC-11 3RMW 1 VERSN REVDAT 1 11-MAY-11 3RMW 0 JRNL AUTH A.CHAIKUAD,D.S.FROESE,G.BERRIDGE,F.VON DELFT,U.OPPERMANN, JRNL AUTH 2 W.W.YUE JRNL TITL CONFORMATIONAL PLASTICITY OF GLYCOGENIN AND ITS JRNL TITL 2 MALTOSACCHARIDE SUBSTRATE DURING GLYCOGEN BIOGENESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 21028 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 22160680 JRNL DOI 10.1073/PNAS.1113921108 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20690 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1116 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1487 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : 1.15000 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): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.122 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2158 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1426 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2924 ; 1.404 ; 2.012 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3443 ; 0.823 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 258 ; 6.947 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;35.602 ;24.353 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 335 ;13.224 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;16.575 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2267 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 412 ; 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): 1266 ; 0.840 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 505 ; 0.222 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2058 ; 1.464 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 892 ; 2.292 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 860 ; 3.478 ; 4.500 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): 1 ; 5.476 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1 ; 5.330 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2917 15.4086 11.5620 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: 0.0181 REMARK 3 T33: 0.0076 T12: 0.0138 REMARK 3 T13: 0.0014 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 2.0301 L22: 2.1253 REMARK 3 L33: 1.5327 L12: 0.0253 REMARK 3 L13: 0.6642 L23: -0.4263 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: -0.0654 S13: -0.0930 REMARK 3 S21: -0.0269 S22: 0.0435 S23: -0.0089 REMARK 3 S31: 0.0729 S32: -0.0245 S33: -0.0287 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 242 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 3.4797 8.5018 0.0435 REMARK 3 T TENSOR REMARK 3 T11: 0.1215 T22: 0.1188 REMARK 3 T33: 0.1922 T12: -0.0772 REMARK 3 T13: -0.0379 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 19.3522 L22: 11.7291 REMARK 3 L33: 13.9901 L12: -4.7534 REMARK 3 L13: -0.0604 L23: 7.7154 REMARK 3 S TENSOR REMARK 3 S11: 0.2964 S12: 0.2099 S13: -1.0775 REMARK 3 S21: 0.1132 S22: -0.1559 S23: 1.1526 REMARK 3 S31: 0.6073 S32: -0.5363 S33: -0.1405 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3RMW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000065128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : FLAT GRAPHITE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 29.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.72800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: PDB ENTRY 3Q4S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG SMEARS (PEG 6K, 8K, 10K), 0.2M REMARK 280 MGCL2, 10% GLYCEROL, 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 28.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.30500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.30500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 56.65000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ILE A 194 REMARK 465 TYR A 195 REMARK 465 SER A 196 REMARK 465 TYR A 197 REMARK 465 LEU A 198 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 HIS A 236 REMARK 465 ASP A 237 REMARK 465 PRO A 238 REMARK 465 ASN A 239 REMARK 465 MET A 240 REMARK 465 THR A 241 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 PHE A 201 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 PHE A 204 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 242 CG ND1 CD2 CE1 NE2 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 MG MG A 265 O HOH A 418 1.66 REMARK 500 O6' UPG A 263 O HOH A 404 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 ASP A 104 33.87 -95.85 REMARK 500 PHE A 171 65.89 -101.10 REMARK 500 ASP A 178 94.65 58.23 REMARK 500 ASN A 188 70.97 -163.64 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 264 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 102 OD2 REMARK 620 2 ASP A 104 OD1 96.4 REMARK 620 3 ASP A 104 OD2 153.5 57.1 REMARK 620 4 HIS A 212 NE2 90.0 93.1 90.3 REMARK 620 5 UPG A 263 O1B 103.5 158.7 102.9 94.3 REMARK 620 6 UPG A 263 O1B 100.2 161.4 106.2 95.1 3.4 REMARK 620 7 UPG A 263 O1A 95.2 84.8 84.4 174.6 85.9 85.4 REMARK 620 8 UPG A 263 O1A 94.9 84.5 84.5 174.7 86.4 85.9 0.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 265 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 151 NE2 REMARK 620 2 GLU A 155 OE1 97.0 REMARK 620 3 HOH A 417 O 92.3 160.6 REMARK 620 4 HOH A 418 O 106.8 85.6 108.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UPG A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 268 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 269 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 270 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 271 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 272 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 275 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 277 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QVB RELATED DB: PDB REMARK 900 HGYG1 (Y195F) WITH UDP,MN REMARK 900 RELATED ID: 3Q4S RELATED DB: PDB REMARK 900 HGYG1 (Y195F) APO FORM REMARK 900 RELATED ID: 3RMV RELATED DB: PDB REMARK 900 HGYG1 (T83M) WITH UDP,MN DBREF 3RMW A 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3RMW SER A 0 UNP P46976 EXPRESSION TAG SEQADV 3RMW MET A 83 UNP P46976 THR 83 ENGINEERED MUTATION SEQRES 1 A 263 SER MET THR ASP GLN ALA PHE VAL THR LEU THR THR ASN SEQRES 2 A 263 ASP ALA TYR ALA LYS GLY ALA LEU VAL LEU GLY SER SER SEQRES 3 A 263 LEU LYS GLN HIS ARG THR THR ARG ARG LEU VAL VAL LEU SEQRES 4 A 263 ALA THR PRO GLN VAL SER ASP SER MET ARG LYS VAL LEU SEQRES 5 A 263 GLU THR VAL PHE ASP GLU VAL ILE MET VAL ASP VAL LEU SEQRES 6 A 263 ASP SER GLY ASP SER ALA HIS LEU THR LEU MET LYS ARG SEQRES 7 A 263 PRO GLU LEU GLY VAL MET LEU THR LYS LEU HIS CYS TRP SEQRES 8 A 263 SER LEU THR GLN TYR SER LYS CYS VAL PHE MET ASP ALA SEQRES 9 A 263 ASP THR LEU VAL LEU ALA ASN ILE ASP ASP LEU PHE ASP SEQRES 10 A 263 ARG GLU GLU LEU SER ALA ALA PRO ASP PRO GLY TRP PRO SEQRES 11 A 263 ASP CYS PHE ASN SER GLY VAL PHE VAL TYR GLN PRO SER SEQRES 12 A 263 VAL GLU THR TYR ASN GLN LEU LEU HIS LEU ALA SER GLU SEQRES 13 A 263 GLN GLY SER PHE ASP GLY GLY ASP GLN GLY ILE LEU ASN SEQRES 14 A 263 THR PHE PHE SER SER TRP ALA THR THR ASP ILE ARG LYS SEQRES 15 A 263 HIS LEU PRO PHE ILE TYR ASN LEU SER SER ILE SER ILE SEQRES 16 A 263 TYR SER TYR LEU PRO ALA PHE LYS VAL PHE GLY ALA SER SEQRES 17 A 263 ALA LYS VAL VAL HIS PHE LEU GLY ARG VAL LYS PRO TRP SEQRES 18 A 263 ASN TYR THR TYR ASP PRO LYS THR LYS SER VAL LYS SER SEQRES 19 A 263 GLU ALA HIS ASP PRO ASN MET THR HIS PRO GLU PHE LEU SEQRES 20 A 263 ILE LEU TRP TRP ASN ILE PHE THR THR ASN VAL LEU PRO SEQRES 21 A 263 LEU LEU GLN HET UPG A 263 72 HET MN A 264 1 HET MG A 265 2 HET EDO A 266 4 HET EDO A 267 4 HET EDO A 268 4 HET EDO A 269 4 HET EDO A 270 4 HET EDO A 271 4 HET EDO A 272 4 HET EDO A 273 4 HET EDO A 274 4 HET EDO A 275 4 HET EDO A 276 4 HET EDO A 277 4 HETNAM UPG URIDINE-5'-DIPHOSPHATE-GLUCOSE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN UPG URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE HETSYN 2 UPG ESTER HETSYN EDO ETHYLENE GLYCOL FORMUL 2 UPG C15 H24 N2 O17 P2 FORMUL 3 MN MN 2+ FORMUL 4 MG MG 2+ FORMUL 5 EDO 12(C2 H6 O2) FORMUL 17 HOH *189(H2 O) HELIX 1 1 ASN A 12 HIS A 29 1 18 HELIX 2 2 SER A 44 PHE A 55 1 12 HELIX 3 3 ALA A 70 ARG A 77 1 8 HELIX 4 4 LEU A 80 HIS A 88 1 9 HELIX 5 5 CYS A 89 LEU A 92 5 4 HELIX 6 6 ILE A 111 ARG A 117 5 7 HELIX 7 7 SER A 142 GLY A 157 1 16 HELIX 8 8 ASP A 163 PHE A 171 1 9 HELIX 9 9 ASP A 178 HIS A 182 5 5 HELIX 10 10 PRO A 184 ASN A 188 5 5 HELIX 11 11 PRO A 199 PHE A 204 1 6 HELIX 12 12 GLY A 205 ALA A 208 5 4 HELIX 13 13 LYS A 218 TYR A 222 5 5 HELIX 14 14 PRO A 243 ASN A 256 1 14 HELIX 15 15 VAL A 257 GLN A 262 5 6 SHEET 1 A 6 GLU A 57 MET A 60 0 SHEET 2 A 6 ARG A 33 ALA A 39 1 N VAL A 37 O ILE A 59 SHEET 3 A 6 MET A 1 THR A 10 1 N PHE A 6 O VAL A 36 SHEET 4 A 6 LYS A 97 MET A 101 1 O MET A 101 N VAL A 7 SHEET 5 A 6 PHE A 132 TYR A 139 -1 O PHE A 137 N PHE A 100 SHEET 6 A 6 SER A 121 PRO A 124 -1 N ALA A 123 O ASN A 133 SHEET 1 B 2 THR A 105 VAL A 107 0 SHEET 2 B 2 VAL A 210 HIS A 212 -1 O VAL A 211 N LEU A 106 SHEET 1 C 2 TYR A 224 ASP A 225 0 SHEET 2 C 2 SER A 230 VAL A 231 -1 O SER A 230 N ASP A 225 LINK OD2 ASP A 102 MN MN A 264 1555 1555 1.99 LINK OD1 ASP A 104 MN MN A 264 1555 1555 2.04 LINK OD2 ASP A 104 MN MN A 264 1555 1555 2.40 LINK NE2 HIS A 151 MG A MG A 265 1555 1555 2.07 LINK OE1 GLU A 155 MG A MG A 265 1555 1555 1.91 LINK NE2 HIS A 212 MN MN A 264 1555 1555 2.14 LINK O1BBUPG A 263 MN MN A 264 1555 1555 1.97 LINK O1BAUPG A 263 MN MN A 264 1555 1555 1.98 LINK O1AAUPG A 263 MN MN A 264 1555 1555 1.98 LINK O1ABUPG A 263 MN MN A 264 1555 1555 1.98 LINK MG A MG A 265 O HOH A 417 1555 1555 1.92 LINK MG B MG A 265 O HOH A 417 1555 1555 2.57 LINK MG A MG A 265 O HOH A 418 1555 1555 2.45 CISPEP 1 GLU A 119 LEU A 120 0 -13.52 SITE 1 AC1 31 LEU A 9 THR A 10 THR A 11 ASN A 12 SITE 2 AC1 31 TYR A 15 LYS A 86 ASP A 102 ALA A 103 SITE 3 AC1 31 ASP A 104 ASN A 133 SER A 134 GLY A 135 SITE 4 AC1 31 ASP A 160 GLY A 162 ASP A 163 GLN A 164 SITE 5 AC1 31 HIS A 212 LEU A 214 GLY A 215 LYS A 218 SITE 6 AC1 31 MN A 264 EDO A 270 HOH A 309 HOH A 343 SITE 7 AC1 31 HOH A 352 HOH A 399 HOH A 400 HOH A 404 SITE 8 AC1 31 HOH A 405 HOH A 461 HOH A 466 SITE 1 AC2 4 ASP A 102 ASP A 104 HIS A 212 UPG A 263 SITE 1 AC3 6 ASP A 3 GLN A 94 HIS A 151 GLU A 155 SITE 2 AC3 6 HOH A 417 HOH A 418 SITE 1 AC4 5 VAL A 61 HIS A 88 SER A 91 LEU A 92 SITE 2 AC4 5 HOH A 340 SITE 1 AC5 5 THR A 93 VAL A 143 HOH A 293 HOH A 446 SITE 2 AC5 5 HOH A 447 SITE 1 AC6 5 PRO A 124 PRO A 129 ASP A 130 HIS A 182 SITE 2 AC6 5 HOH A 348 SITE 1 AC7 6 GLU A 119 LEU A 120 SER A 173 TRP A 174 SITE 2 AC7 6 LYS A 181 HOH A 312 SITE 1 AC8 5 VAL A 82 LYS A 86 GLY A 161 ASP A 163 SITE 2 AC8 5 UPG A 263 SITE 1 AC9 5 THR A 2 GLN A 94 GLN A 148 HIS A 151 SITE 2 AC9 5 HOH A 334 SITE 1 BC1 4 PHE A 170 PHE A 171 HOH A 283 HOH A 356 SITE 1 BC2 5 ASP A 56 GLU A 57 VAL A 58 HOH A 436 SITE 2 BC2 5 HOH A 438 SITE 1 BC3 4 PRO A 41 ASP A 62 GLN A 262 HOH A 336 SITE 1 BC4 3 ASP A 45 LYS A 49 GLU A 52 SITE 1 BC5 3 ASP A 65 SER A 66 HOH A 371 SITE 1 BC6 3 ASP A 56 GLU A 144 HOH A 439 CRYST1 56.650 100.610 49.100 90.00 90.00 90.00 P 21 21 2 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 0.017652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020367 0.00000