HEADER TRANSFERASE 04-OCT-11 3U2T TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH TITLE 2 MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGENIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLYCOGENIN (RESIDUES 1-262); COMPND 5 SYNONYM: GN-1, GN1; COMPND 6 EC: 2.4.1.186; COMPND 7 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: 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,E.KRYSZTOFINSKA,F.VON DELFT,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,U.OPPERMANN,W.W.YUE,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 5 13-SEP-23 3U2T 1 REMARK SEQADV LINK REVDAT 4 11-JAN-12 3U2T 1 JRNL REVDAT 3 28-DEC-11 3U2T 1 JRNL REVDAT 2 14-DEC-11 3U2T 1 REVDAT 1 02-NOV-11 3U2T 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17417 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1247 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : -2.41000 REMARK 3 B33 (A**2) : 2.62000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2093 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1383 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2845 ; 1.521 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3384 ; 1.058 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 5.921 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 89 ;37.112 ;24.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 339 ;13.286 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;15.112 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 330 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2289 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 422 ; 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): 1286 ; 0.556 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 514 ; 0.124 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2089 ; 1.011 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 807 ; 1.669 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 753 ; 2.495 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 -2 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0266 14.9153 11.2567 REMARK 3 T TENSOR REMARK 3 T11: 0.0340 T22: 0.0099 REMARK 3 T33: 0.0113 T12: 0.0098 REMARK 3 T13: 0.0023 T23: -0.0037 REMARK 3 L TENSOR REMARK 3 L11: 2.2461 L22: 2.1929 REMARK 3 L33: 1.5193 L12: -0.0767 REMARK 3 L13: 0.3233 L23: -0.4016 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: 0.0514 S13: -0.0106 REMARK 3 S21: -0.1257 S22: -0.0040 S23: 0.0775 REMARK 3 S31: 0.0112 S32: -0.0331 S33: -0.0149 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 240 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 4.6404 8.5414 -0.3722 REMARK 3 T TENSOR REMARK 3 T11: 0.1651 T22: 0.1633 REMARK 3 T33: 0.1168 T12: -0.0686 REMARK 3 T13: -0.0861 T23: -0.0257 REMARK 3 L TENSOR REMARK 3 L11: 13.5866 L22: 19.9093 REMARK 3 L33: 7.8923 L12: -9.0923 REMARK 3 L13: 1.0740 L23: 0.5078 REMARK 3 S TENSOR REMARK 3 S11: 0.1110 S12: 0.1760 S13: -0.8154 REMARK 3 S21: -0.7604 S22: -0.0325 S23: 1.2098 REMARK 3 S31: 0.0525 S32: -0.4543 S33: -0.0785 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 3U2T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 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 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 : 18330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 38.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 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) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.65200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 44.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5% PEG SMEARS, 0.2M LI2(SO4), 0.05M REMARK 280 ZNCL2, 0.1M BIS-TRIS, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 29.17500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.17500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.53000 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 300 REMARK: THE OTHER SUBUNIT IN THE DIMER PAIR IS GENERATED BY THE TWO REMARK 300 FOLD AXIS: -X,-Y,Z 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: 3340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 58.35000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 400 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 ILE A 194 REMARK 465 TYR A 195 REMARK 465 SER A 196 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 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 -2 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 197 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 216 CG CD NE CZ NH1 NH2 REMARK 470 MET A 240 CG SD CE 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 NH2 ARG A 117 O HOH A 305 2.09 REMARK 500 OE1 GLU A 57 OH TYR A 95 2.13 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 PHE A 171 56.44 -99.75 REMARK 500 ASP A 178 91.89 51.79 REMARK 500 ASN A 188 69.27 -160.41 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 263 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 102 OD2 REMARK 620 2 ASP A 104 OD1 102.6 REMARK 620 3 ASP A 104 OD2 144.9 52.8 REMARK 620 4 HIS A 212 NE2 99.5 83.6 101.5 REMARK 620 5 HOH A 268 O 106.5 148.3 95.6 103.5 REMARK 620 6 HOH A 269 O 87.3 88.4 69.4 170.5 80.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QVB RELATED DB: PDB REMARK 900 HGYG1 (Y195F) WITH UDP,MN IN OPEN FORM REMARK 900 RELATED ID: 3Q4S RELATED DB: PDB REMARK 900 HGYG1 (Y195F) APO FORM REMARK 900 RELATED ID: 3RMW RELATED DB: PDB REMARK 900 HGYG1 (T83M) WITH UDPG, MN REMARK 900 RELATED ID: 3RMV RELATED DB: PDB REMARK 900 HGYG1 (T83M) WITH UDP, MN REMARK 900 RELATED ID: 3T7M RELATED DB: PDB REMARK 900 HGYG1 COMPLEXED WITH MN AND UDP REMARK 900 RELATED ID: 3T7O RELATED DB: PDB REMARK 900 HGYG1 COMPLEXED WITH MN, UDPG AND GLUCOSE REMARK 900 RELATED ID: 3T7N RELATED DB: PDB REMARK 900 HGYG1 COMPLEXED WITH MN AND UDP REMARK 900 RELATED ID: 3U2U RELATED DB: PDB REMARK 900 RELATED ID: 3U2V RELATED DB: PDB REMARK 900 RELATED ID: 3U2W RELATED DB: PDB REMARK 900 RELATED ID: 3U2X RELATED DB: PDB DBREF 3U2T A 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3U2T MET A -21 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -20 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -19 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -18 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -17 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -16 UNP P46976 EXPRESSION TAG SEQADV 3U2T HIS A -15 UNP P46976 EXPRESSION TAG SEQADV 3U2T SER A -14 UNP P46976 EXPRESSION TAG SEQADV 3U2T SER A -13 UNP P46976 EXPRESSION TAG SEQADV 3U2T GLY A -12 UNP P46976 EXPRESSION TAG SEQADV 3U2T VAL A -11 UNP P46976 EXPRESSION TAG SEQADV 3U2T ASP A -10 UNP P46976 EXPRESSION TAG SEQADV 3U2T LEU A -9 UNP P46976 EXPRESSION TAG SEQADV 3U2T GLY A -8 UNP P46976 EXPRESSION TAG SEQADV 3U2T THR A -7 UNP P46976 EXPRESSION TAG SEQADV 3U2T GLU A -6 UNP P46976 EXPRESSION TAG SEQADV 3U2T ASN A -5 UNP P46976 EXPRESSION TAG SEQADV 3U2T LEU A -4 UNP P46976 EXPRESSION TAG SEQADV 3U2T TYR A -3 UNP P46976 EXPRESSION TAG SEQADV 3U2T PHE A -2 UNP P46976 EXPRESSION TAG SEQADV 3U2T GLN A -1 UNP P46976 EXPRESSION TAG SEQADV 3U2T SER A 0 UNP P46976 EXPRESSION TAG SEQRES 1 A 284 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 284 GLY THR GLU ASN LEU TYR PHE GLN SER MET THR ASP GLN SEQRES 3 A 284 ALA PHE VAL THR LEU THR THR ASN ASP ALA TYR ALA LYS SEQRES 4 A 284 GLY ALA LEU VAL LEU GLY SER SER LEU LYS GLN HIS ARG SEQRES 5 A 284 THR THR ARG ARG LEU VAL VAL LEU ALA THR PRO GLN VAL SEQRES 6 A 284 SER ASP SER MET ARG LYS VAL LEU GLU THR VAL PHE ASP SEQRES 7 A 284 GLU VAL ILE MET VAL ASP VAL LEU ASP SER GLY ASP SER SEQRES 8 A 284 ALA HIS LEU THR LEU MET LYS ARG PRO GLU LEU GLY VAL SEQRES 9 A 284 THR LEU THR LYS LEU HIS CYS TRP SER LEU THR GLN TYR SEQRES 10 A 284 SER LYS CYS VAL PHE MET ASP ALA ASP THR LEU VAL LEU SEQRES 11 A 284 ALA ASN ILE ASP ASP LEU PHE ASP ARG GLU GLU LEU SER SEQRES 12 A 284 ALA ALA PRO ASP PRO GLY TRP PRO ASP CYS PHE ASN SER SEQRES 13 A 284 GLY VAL PHE VAL TYR GLN PRO SER VAL GLU THR TYR ASN SEQRES 14 A 284 GLN LEU LEU HIS LEU ALA SER GLU GLN GLY SER PHE ASP SEQRES 15 A 284 GLY GLY ASP GLN GLY ILE LEU ASN THR PHE PHE SER SER SEQRES 16 A 284 TRP ALA THR THR ASP ILE ARG LYS HIS LEU PRO PHE ILE SEQRES 17 A 284 TYR ASN LEU SER SER ILE SER ILE TYR SER TYR LEU PRO SEQRES 18 A 284 ALA PHE LYS VAL PHE GLY ALA SER ALA LYS VAL VAL HIS SEQRES 19 A 284 PHE LEU GLY ARG VAL LYS PRO TRP ASN TYR THR TYR ASP SEQRES 20 A 284 PRO LYS THR LYS SER VAL LYS SER GLU ALA HIS ASP PRO SEQRES 21 A 284 ASN MET THR HIS PRO GLU PHE LEU ILE LEU TRP TRP ASN SEQRES 22 A 284 ILE PHE THR THR ASN VAL LEU PRO LEU LEU GLN HET MN A 263 1 HET EDO A 264 4 HET EDO A 265 4 HET EDO A 266 4 HET EDO A 267 4 HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MN MN 2+ FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *140(H2 O) HELIX 1 1 ASN A 12 HIS A 29 1 18 HELIX 2 2 SER A 44 THR A 53 1 10 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 GLY A 162 PHE A 171 1 10 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 LEU A 198 GLY A 205 1 8 HELIX 12 12 ALA A 206 ALA A 208 5 3 HELIX 13 13 LYS A 218 TYR A 222 5 5 HELIX 14 14 PRO A 243 VAL A 257 1 15 HELIX 15 15 LEU A 258 LEU A 261 5 4 SHEET 1 A 6 GLU A 57 MET A 60 0 SHEET 2 A 6 ARG A 33 ALA A 39 1 N ALA A 39 O ILE A 59 SHEET 3 A 6 MET A 1 THR A 10 1 N PHE A 6 O ARG A 34 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 TYR A 139 N CYS A 98 SHEET 6 A 6 SER A 121 PRO A 124 -1 N ALA A 123 O ASN A 133 SHEET 1 B 3 THR A 105 VAL A 107 0 SHEET 2 B 3 VAL A 210 HIS A 212 -1 O VAL A 211 N LEU A 106 SHEET 3 B 3 LEU A 189 SER A 190 1 N LEU A 189 O HIS A 212 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 263 1555 1555 1.99 LINK OD1 ASP A 104 MN MN A 263 1555 1555 2.30 LINK OD2 ASP A 104 MN MN A 263 1555 1555 2.54 LINK NE2 HIS A 212 MN MN A 263 1555 1555 2.13 LINK MN MN A 263 O HOH A 268 1555 1555 2.35 LINK MN MN A 263 O HOH A 269 1555 1555 2.51 CISPEP 1 GLU A 119 LEU A 120 0 -8.29 SITE 1 AC1 5 ASP A 102 ASP A 104 HIS A 212 HOH A 268 SITE 2 AC1 5 HOH A 269 SITE 1 AC2 2 ARG A 33 HOH A 349 SITE 1 AC3 5 GLU A 119 LEU A 120 SER A 173 LYS A 181 SITE 2 AC3 5 HOH A 325 SITE 1 AC4 4 THR A 93 SER A 142 VAL A 143 GLU A 144 SITE 1 AC5 2 HIS A 29 ASN A 110 CRYST1 58.350 101.060 47.830 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 0.017138 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020907 0.00000 CONECT 819 2029 CONECT 831 2029 CONECT 832 2029 CONECT 1657 2029 CONECT 2029 819 831 832 1657 CONECT 2029 2046 2047 CONECT 2030 2031 2032 CONECT 2031 2030 CONECT 2032 2030 2033 CONECT 2033 2032 CONECT 2034 2035 2036 CONECT 2035 2034 CONECT 2036 2034 2037 CONECT 2037 2036 CONECT 2038 2039 2040 CONECT 2039 2038 CONECT 2040 2038 2041 CONECT 2041 2040 CONECT 2042 2043 2044 CONECT 2043 2042 CONECT 2044 2042 2045 CONECT 2045 2044 CONECT 2046 2029 CONECT 2047 2029 MASTER 422 0 5 15 11 0 7 6 2164 1 24 22 END