HEADER TRANSFERASE 04-OCT-11 3U2W TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH TITLE 2 MANGANESE AND GLUCOSE OR A GLUCAL SPECIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGENIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: GLYCOGENIN (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: 511693; 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, GLUCAL 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 6 13-SEP-23 3U2W 1 HETSYN REVDAT 5 29-JUL-20 3U2W 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE REVDAT 4 11-JAN-12 3U2W 1 JRNL REVDAT 3 28-DEC-11 3U2W 1 JRNL REVDAT 2 14-DEC-11 3U2W 1 REVDAT 1 02-NOV-11 3U2W 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. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 55123 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2946 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) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3964 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.4220 REMARK 3 BIN FREE R VALUE SET COUNT : 216 REMARK 3 BIN FREE R VALUE : 0.4700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 105 REMARK 3 SOLVENT ATOMS : 504 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : 1.43000 REMARK 3 B33 (A**2) : -0.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.72000 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): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.496 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4365 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2840 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5968 ; 1.499 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6965 ; 0.974 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.134 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;35.656 ;24.225 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 683 ;11.885 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;12.248 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 694 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4750 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 880 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 1 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 34.7644 3.5738 57.6129 REMARK 3 T TENSOR REMARK 3 T11: 0.0051 T22: 0.0132 REMARK 3 T33: 0.0176 T12: -0.0066 REMARK 3 T13: -0.0085 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.5390 L22: 0.8361 REMARK 3 L33: 1.7744 L12: -0.0052 REMARK 3 L13: 0.2214 L23: -0.0204 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: -0.0840 S13: -0.0210 REMARK 3 S21: 0.0018 S22: -0.0088 S23: -0.0327 REMARK 3 S31: -0.0082 S32: 0.0770 S33: -0.0252 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 190 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 14.5967 5.9351 57.4097 REMARK 3 T TENSOR REMARK 3 T11: 0.0674 T22: 0.1987 REMARK 3 T33: 0.0851 T12: 0.0112 REMARK 3 T13: -0.0299 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 3.0914 L22: 1.6582 REMARK 3 L33: 1.9796 L12: -0.4369 REMARK 3 L13: -1.2488 L23: 0.3028 REMARK 3 S TENSOR REMARK 3 S11: 0.1018 S12: 0.1859 S13: -0.0166 REMARK 3 S21: -0.2187 S22: -0.1131 S23: 0.2712 REMARK 3 S31: -0.0892 S32: -0.5788 S33: 0.0114 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 189 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1828 -7.1580 23.3279 REMARK 3 T TENSOR REMARK 3 T11: 0.0104 T22: 0.0089 REMARK 3 T33: 0.0252 T12: -0.0074 REMARK 3 T13: 0.0007 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.2297 L22: 1.4942 REMARK 3 L33: 1.8825 L12: 0.4498 REMARK 3 L13: 0.4776 L23: -0.1681 REMARK 3 S TENSOR REMARK 3 S11: 0.0276 S12: 0.0323 S13: -0.0925 REMARK 3 S21: -0.0106 S22: 0.0159 S23: 0.0026 REMARK 3 S31: 0.1358 S32: -0.0782 S33: -0.0435 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 190 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2384 12.7199 25.1156 REMARK 3 T TENSOR REMARK 3 T11: 0.1684 T22: 0.1178 REMARK 3 T33: 0.1671 T12: 0.0125 REMARK 3 T13: -0.0206 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 0.7353 L22: 0.6199 REMARK 3 L33: 4.7663 L12: 0.5820 REMARK 3 L13: 1.3539 L23: 1.2677 REMARK 3 S TENSOR REMARK 3 S11: -0.1780 S12: 0.0393 S13: 0.2685 REMARK 3 S21: -0.0856 S22: -0.0810 S23: 0.1503 REMARK 3 S31: -0.7004 S32: -0.3396 S33: 0.2589 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 REMARK 4 REMARK 4 3U2W 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_1000068237. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 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 : 58070 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 22.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.2M LI2(SO4), 0.1M REMARK 280 TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.09000 REMARK 290 SMTRY3 2 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: 5870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 SER A 0 REMARK 465 SER B 0 REMARK 465 ASP B 68 REMARK 465 SER B 69 REMARK 465 ALA B 70 REMARK 465 HIS B 71 REMARK 465 LEU B 72 REMARK 465 THR B 73 REMARK 465 LEU B 74 REMARK 465 MET B 75 REMARK 465 LYS B 76 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 1 CG SD CE REMARK 470 TYR A 197 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 SER A 233 OG REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 227 CG CD CE NZ REMARK 470 LYS B 229 CG CD CE NZ REMARK 470 GLU B 234 CG CD OE1 OE2 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 O3 GOL A 265 O1 GLC A 267 2.00 REMARK 500 O HOH A 351 O HOH A 400 2.18 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 ASP A 104 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 104 CB - CG - OD2 ANGL. DEV. = 6.5 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 A 104 36.08 -95.83 REMARK 500 PHE A 171 44.07 -96.70 REMARK 500 ASN A 188 69.78 -163.90 REMARK 500 PHE A 213 49.93 -80.77 REMARK 500 ALA A 235 -151.66 48.80 REMARK 500 ASP A 237 102.57 -160.71 REMARK 500 ASP B 104 31.88 -99.73 REMARK 500 PHE B 171 44.92 -97.99 REMARK 500 THR B 177 -60.88 -90.73 REMARK 500 ASN B 188 78.70 -172.74 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 94.4 REMARK 620 3 ASP A 104 OD2 150.5 56.1 REMARK 620 4 HIS A 212 NE2 93.4 94.3 89.4 REMARK 620 5 UDP A 264 O3B 106.3 158.2 103.0 91.2 REMARK 620 6 UDP A 264 O2A 95.4 84.4 82.6 171.2 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 263 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 102 OD2 REMARK 620 2 ASP B 104 OD1 94.4 REMARK 620 3 ASP B 104 OD2 153.0 59.7 REMARK 620 4 HIS B 212 NE2 93.9 93.3 95.0 REMARK 620 5 UDP B 264 O1A 90.4 84.5 80.3 175.4 REMARK 620 6 UDP B 264 O1B 101.8 162.5 103.3 92.2 88.8 REMARK 620 N 1 2 3 4 5 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: 3U2T RELATED DB: PDB REMARK 900 RELATED ID: 3U2U RELATED DB: PDB REMARK 900 RELATED ID: 3U2V RELATED DB: PDB REMARK 900 RELATED ID: 3U2X RELATED DB: PDB DBREF 3U2W A 1 262 UNP P46976 GLYG_HUMAN 1 262 DBREF 3U2W B 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3U2W SER A 0 UNP P46976 EXPRESSION TAG SEQADV 3U2W PHE A 195 UNP P46976 TYR 195 ENGINEERED MUTATION SEQADV 3U2W SER B 0 UNP P46976 EXPRESSION TAG SEQADV 3U2W PHE B 195 UNP P46976 TYR 195 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 THR 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 PHE 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 SEQRES 1 B 263 SER MET THR ASP GLN ALA PHE VAL THR LEU THR THR ASN SEQRES 2 B 263 ASP ALA TYR ALA LYS GLY ALA LEU VAL LEU GLY SER SER SEQRES 3 B 263 LEU LYS GLN HIS ARG THR THR ARG ARG LEU VAL VAL LEU SEQRES 4 B 263 ALA THR PRO GLN VAL SER ASP SER MET ARG LYS VAL LEU SEQRES 5 B 263 GLU THR VAL PHE ASP GLU VAL ILE MET VAL ASP VAL LEU SEQRES 6 B 263 ASP SER GLY ASP SER ALA HIS LEU THR LEU MET LYS ARG SEQRES 7 B 263 PRO GLU LEU GLY VAL THR LEU THR LYS LEU HIS CYS TRP SEQRES 8 B 263 SER LEU THR GLN TYR SER LYS CYS VAL PHE MET ASP ALA SEQRES 9 B 263 ASP THR LEU VAL LEU ALA ASN ILE ASP ASP LEU PHE ASP SEQRES 10 B 263 ARG GLU GLU LEU SER ALA ALA PRO ASP PRO GLY TRP PRO SEQRES 11 B 263 ASP CYS PHE ASN SER GLY VAL PHE VAL TYR GLN PRO SER SEQRES 12 B 263 VAL GLU THR TYR ASN GLN LEU LEU HIS LEU ALA SER GLU SEQRES 13 B 263 GLN GLY SER PHE ASP GLY GLY ASP GLN GLY ILE LEU ASN SEQRES 14 B 263 THR PHE PHE SER SER TRP ALA THR THR ASP ILE ARG LYS SEQRES 15 B 263 HIS LEU PRO PHE ILE TYR ASN LEU SER SER ILE SER ILE SEQRES 16 B 263 PHE SER TYR LEU PRO ALA PHE LYS VAL PHE GLY ALA SER SEQRES 17 B 263 ALA LYS VAL VAL HIS PHE LEU GLY ARG VAL LYS PRO TRP SEQRES 18 B 263 ASN TYR THR TYR ASP PRO LYS THR LYS SER VAL LYS SER SEQRES 19 B 263 GLU ALA HIS ASP PRO ASN MET THR HIS PRO GLU PHE LEU SEQRES 20 B 263 ILE LEU TRP TRP ASN ILE PHE THR THR ASN VAL LEU PRO SEQRES 21 B 263 LEU LEU GLN HET MN A 263 1 HET UDP A 264 25 HET GOL A 265 6 HET GOL A 266 6 HET GLC A 267 12 HET LCN A 268 11 HET MN B 263 1 HET UDP B 264 25 HET GOL B 265 6 HET GLC B 266 12 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM LCN 1,5-ANHYDRO-D-ARABINO-HEX-1-ENITOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 MN 2(MN 2+) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 7 GLC 2(C6 H12 O6) FORMUL 8 LCN C6 H10 O5 FORMUL 13 HOH *504(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 ASP A 68 LYS A 76 1 9 HELIX 4 4 GLU A 79 LEU A 92 5 14 HELIX 5 5 ILE A 111 ARG A 117 5 7 HELIX 6 6 SER A 142 GLY A 157 1 16 HELIX 7 7 GLY A 162 PHE A 171 1 10 HELIX 8 8 ASP A 178 HIS A 182 5 5 HELIX 9 9 PRO A 184 ASN A 188 5 5 HELIX 10 10 LEU A 198 GLY A 205 1 8 HELIX 11 11 ALA A 206 ALA A 208 5 3 HELIX 12 12 LYS A 218 TYR A 222 5 5 HELIX 13 13 ASP A 237 THR A 241 5 5 HELIX 14 14 PRO A 243 VAL A 257 1 15 HELIX 15 15 LEU A 258 GLN A 262 5 5 HELIX 16 16 ASN B 12 HIS B 29 1 18 HELIX 17 17 SER B 44 PHE B 55 1 12 HELIX 18 18 ARG B 77 LEU B 92 5 16 HELIX 19 19 ILE B 111 ARG B 117 5 7 HELIX 20 20 SER B 142 GLN B 156 1 15 HELIX 21 21 GLY B 162 PHE B 171 1 10 HELIX 22 22 ASP B 178 HIS B 182 5 5 HELIX 23 23 PRO B 184 ASN B 188 5 5 HELIX 24 24 SER B 191 TYR B 197 1 7 HELIX 25 25 TYR B 197 GLY B 205 1 9 HELIX 26 26 ALA B 206 ALA B 208 5 3 HELIX 27 27 LYS B 218 TYR B 222 5 5 HELIX 28 28 HIS B 242 VAL B 257 1 16 HELIX 29 29 VAL B 257 GLN B 262 1 6 SHEET 1 A 6 GLU A 57 MET A 60 0 SHEET 2 A 6 ARG A 34 ALA A 39 1 N VAL A 37 O ILE A 59 SHEET 3 A 6 GLN A 4 THR A 10 1 N THR A 8 O LEU A 38 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 SER A 121 O VAL A 138 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 SHEET 1 D 6 GLU B 57 MET B 60 0 SHEET 2 D 6 ARG B 34 ALA B 39 1 N VAL B 37 O ILE B 59 SHEET 3 D 6 GLN B 4 THR B 10 1 N PHE B 6 O VAL B 36 SHEET 4 D 6 LYS B 97 MET B 101 1 O MET B 101 N VAL B 7 SHEET 5 D 6 PHE B 132 TYR B 139 -1 O PHE B 137 N PHE B 100 SHEET 6 D 6 SER B 121 PRO B 124 -1 N ALA B 123 O ASN B 133 SHEET 1 E 3 THR B 105 VAL B 107 0 SHEET 2 E 3 VAL B 210 HIS B 212 -1 O VAL B 211 N LEU B 106 SHEET 3 E 3 LEU B 189 SER B 190 1 N LEU B 189 O HIS B 212 SHEET 1 F 2 THR B 223 ASP B 225 0 SHEET 2 F 2 SER B 230 LYS B 232 -1 O LYS B 232 N THR B 223 LINK OD2 ASP A 102 MN MN A 263 1555 1555 2.03 LINK OD1 ASP A 104 MN MN A 263 1555 1555 2.09 LINK OD2 ASP A 104 MN MN A 263 1555 1555 2.47 LINK NE2 HIS A 212 MN MN A 263 1555 1555 2.17 LINK MN MN A 263 O3B UDP A 264 1555 1555 2.00 LINK MN MN A 263 O2A UDP A 264 1555 1555 2.03 LINK OD2 ASP B 102 MN MN B 263 1555 1555 2.07 LINK OD1 ASP B 104 MN MN B 263 1555 1555 2.06 LINK OD2 ASP B 104 MN MN B 263 1555 1555 2.11 LINK NE2 HIS B 212 MN MN B 263 1555 1555 2.16 LINK MN MN B 263 O1A UDP B 264 1555 1555 2.03 LINK MN MN B 263 O1B UDP B 264 1555 1555 2.04 CISPEP 1 GLU A 119 LEU A 120 0 -11.59 CISPEP 2 GLU B 119 LEU B 120 0 -8.86 CRYST1 47.290 80.180 69.530 90.00 100.67 90.00 P 1 21 1 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 0.021146 0.000000 0.003984 0.00000 SCALE2 0.000000 0.012472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014635 0.00000