HEADER TRANSFERASE 04-OCT-11 3U2V TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH TITLE 2 MANGANESE, UDP AND MALTOHEXAOSE 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 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, OLIGOSACCHARIDE, SUGAR CHAIN, RETAINING ANOMERIC KEYWDS 4 CONFIGURATION 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 7 20-NOV-24 3U2V 1 REMARK REVDAT 6 13-SEP-23 3U2V 1 HETSYN REVDAT 5 29-JUL-20 3U2V 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 11-JAN-12 3U2V 1 JRNL REVDAT 3 28-DEC-11 3U2V 1 JRNL REVDAT 2 14-DEC-11 3U2V 1 REVDAT 1 07-DEC-11 3U2V 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 81446 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4306 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5801 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 296 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 242 REMARK 3 SOLVENT ATOMS : 608 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.68000 REMARK 3 B12 (A**2) : -0.84000 REMARK 3 B13 (A**2) : 0.36000 REMARK 3 B23 (A**2) : 0.59000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.782 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4590 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2981 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6287 ; 1.514 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7280 ; 0.930 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 550 ; 5.852 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;36.062 ;24.225 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 696 ;11.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;10.471 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 767 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4838 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 909 ; 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 0 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): 49.8074 27.1318 16.4494 REMARK 3 T TENSOR REMARK 3 T11: 0.0460 T22: 0.0258 REMARK 3 T33: 0.0401 T12: -0.0049 REMARK 3 T13: -0.0010 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.1764 L22: 0.2927 REMARK 3 L33: 0.9276 L12: 0.2078 REMARK 3 L13: -0.1129 L23: 0.0496 REMARK 3 S TENSOR REMARK 3 S11: -0.0057 S12: 0.0038 S13: -0.0125 REMARK 3 S21: -0.0178 S22: 0.0095 S23: 0.0000 REMARK 3 S31: -0.0773 S32: 0.0280 S33: -0.0039 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 214 A 262 REMARK 3 ORIGIN FOR THE GROUP (A): 51.2760 7.1981 11.3090 REMARK 3 T TENSOR REMARK 3 T11: 0.0928 T22: 0.0064 REMARK 3 T33: 0.0402 T12: 0.0127 REMARK 3 T13: -0.0023 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.0703 L22: 1.9111 REMARK 3 L33: 1.4483 L12: 0.3352 REMARK 3 L13: -0.0653 L23: 0.2888 REMARK 3 S TENSOR REMARK 3 S11: -0.0228 S12: -0.0038 S13: -0.0100 REMARK 3 S21: 0.0376 S22: -0.0119 S23: -0.0649 REMARK 3 S31: 0.1868 S32: 0.0170 S33: 0.0347 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 0 B 213 REMARK 3 ORIGIN FOR THE GROUP (A): 38.4767 18.1217 47.8228 REMARK 3 T TENSOR REMARK 3 T11: 0.0324 T22: 0.0424 REMARK 3 T33: 0.0373 T12: -0.0037 REMARK 3 T13: 0.0081 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.3479 L22: 0.1265 REMARK 3 L33: 0.8809 L12: 0.1377 REMARK 3 L13: 0.1265 L23: -0.1202 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: -0.0021 S13: 0.0158 REMARK 3 S21: 0.0201 S22: -0.0112 S23: -0.0076 REMARK 3 S31: 0.0121 S32: -0.0678 S33: 0.0076 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 214 B 262 REMARK 3 ORIGIN FOR THE GROUP (A): 57.4125 11.9659 52.8274 REMARK 3 T TENSOR REMARK 3 T11: 0.0514 T22: 0.0865 REMARK 3 T33: 0.0447 T12: 0.0212 REMARK 3 T13: 0.0227 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.9471 L22: 0.0752 REMARK 3 L33: 1.0872 L12: -0.3027 REMARK 3 L13: -0.1207 L23: -0.0926 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: 0.0926 S13: -0.0580 REMARK 3 S21: 0.0143 S22: -0.0534 S23: 0.0240 REMARK 3 S31: 0.0947 S32: 0.2718 S33: 0.0655 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 3U2V 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_1000068236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-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) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : KIRKPATRICK BAEZ BIMORPH MIRROR REMARK 200 PAIR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC Q315 3X3 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85751 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 (%): 49.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULPHATE, 0.1M HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 10960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 SER A 0 OG REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 HIS A 236 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 0 OG REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 232 CG CD CE NZ REMARK 470 HIS B 236 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 O HOH B 336 O HOH B 654 2.04 REMARK 500 O HOH B 463 O HOH B 556 2.05 REMARK 500 O1 GOL B 274 O HOH B 608 2.06 REMARK 500 OH TYR B 195 O5 GLC D 1 2.07 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 - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 178 85.66 66.89 REMARK 500 ASN A 188 65.92 -163.97 REMARK 500 ASP B 178 85.12 66.45 REMARK 500 ASN B 188 68.42 -160.96 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 269 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 102 OD2 REMARK 620 2 ASP A 104 OD1 96.6 REMARK 620 3 ASP A 104 OD2 153.1 56.7 REMARK 620 4 HIS A 212 NE2 94.9 94.3 91.2 REMARK 620 5 UDP A 270 O3B 102.7 159.1 103.3 92.0 REMARK 620 6 UDP A 270 O2A 92.6 85.0 82.2 172.5 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 269 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 102 OD2 REMARK 620 2 ASP B 104 OD1 95.2 REMARK 620 3 ASP B 104 OD2 153.0 57.9 REMARK 620 4 HIS B 212 NE2 95.5 94.8 89.4 REMARK 620 5 UDP B 270 O1B 102.6 159.5 103.5 93.5 REMARK 620 6 UDP B 270 O2A 92.4 83.2 82.9 172.0 85.9 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: 3U2W RELATED DB: PDB REMARK 900 RELATED ID: 3U2X RELATED DB: PDB DBREF 3U2V A 1 262 UNP P46976 GLYG_HUMAN 1 262 DBREF 3U2V B 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3U2V SER A 0 UNP P46976 EXPRESSION TAG SEQADV 3U2V SER B 0 UNP P46976 EXPRESSION TAG 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 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 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 TYR 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 GLC C 1 11 HET GLC C 2 11 HET GLC C 3 11 HET GLC C 4 11 HET GLC C 5 11 HET GLC C 6 11 HET GLC D 1 11 HET GLC D 2 11 HET GLC D 3 11 HET GLC D 4 11 HET GLC D 5 11 HET GLC D 6 11 HET MN A 269 1 HET UDP A 270 25 HET GOL A 271 6 HET GOL A 272 6 HET SO4 A 273 5 HET MN B 269 1 HET UDP B 270 25 HET GOL B 271 6 HET GOL B 272 6 HET GOL B 273 6 HET GOL B 274 6 HET GOL B 275 12 HET GOL B 276 6 HET SO4 B 277 5 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GLC 12(C6 H12 O6) FORMUL 5 MN 2(MN 2+) FORMUL 6 UDP 2(C9 H14 N2 O12 P2) FORMUL 7 GOL 8(C3 H8 O3) FORMUL 9 SO4 2(O4 S 2-) FORMUL 19 HOH *608(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 MET A 75 1 8 HELIX 4 4 LYS A 76 LEU A 92 5 17 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 SER A 191 TYR A 197 1 7 HELIX 11 11 TYR A 197 GLY A 205 1 9 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 ASP A 237 THR A 241 5 5 HELIX 15 15 PRO A 243 VAL A 257 1 15 HELIX 16 16 LEU A 258 GLN A 262 5 5 HELIX 17 17 ASN B 12 HIS B 29 1 18 HELIX 18 18 SER B 44 PHE B 55 1 12 HELIX 19 19 ASP B 68 MET B 75 1 8 HELIX 20 20 GLU B 79 LEU B 92 5 14 HELIX 21 21 ILE B 111 ARG B 117 5 7 HELIX 22 22 SER B 142 GLN B 156 1 15 HELIX 23 23 GLY B 162 PHE B 171 1 10 HELIX 24 24 ASP B 178 HIS B 182 5 5 HELIX 25 25 PRO B 184 ASN B 188 5 5 HELIX 26 26 SER B 191 TYR B 197 1 7 HELIX 27 27 TYR B 197 GLY B 205 1 9 HELIX 28 28 ALA B 206 ALA B 208 5 3 HELIX 29 29 LYS B 218 TYR B 222 5 5 HELIX 30 30 ASP B 237 THR B 241 5 5 HELIX 31 31 PRO B 243 VAL B 257 1 15 HELIX 32 32 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 10 O LEU A 38 SHEET 4 A 6 LYS A 97 MET A 101 1 O VAL A 99 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 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 SHEET 1 D 6 GLU B 57 MET B 60 0 SHEET 2 D 6 ARG B 33 ALA B 39 1 N ALA B 39 O ILE B 59 SHEET 3 D 6 MET B 1 THR B 10 1 N THR B 8 O LEU B 38 SHEET 4 D 6 LYS B 97 MET B 101 1 O VAL B 99 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 TYR B 224 ASP B 225 0 SHEET 2 F 2 SER B 230 VAL B 231 -1 O SER B 230 N ASP B 225 LINK OH TYR A 195 C1 GLC C 1 1555 1555 1.45 LINK OH TYR B 195 C1 GLC D 1 1555 1555 1.45 LINK O4 GLC C 1 C1 GLC C 2 1555 1555 1.45 LINK O4 GLC C 2 C1 GLC C 3 1555 1555 1.47 LINK O4 GLC C 3 C1 GLC C 4 1555 1555 1.46 LINK O4 GLC C 4 C1 GLC C 5 1555 1555 1.45 LINK O4 GLC C 5 C1 GLC C 6 1555 1555 1.44 LINK O4 GLC D 1 C1 GLC D 2 1555 1555 1.45 LINK O4 GLC D 2 C1 GLC D 3 1555 1555 1.46 LINK O4 GLC D 3 C1 GLC D 4 1555 1555 1.45 LINK O4 GLC D 4 C1 GLC D 5 1555 1555 1.45 LINK O4 GLC D 5 C1 GLC D 6 1555 1555 1.43 LINK OD2 ASP A 102 MN MN A 269 1555 1555 2.06 LINK OD1 ASP A 104 MN MN A 269 1555 1555 2.09 LINK OD2 ASP A 104 MN MN A 269 1555 1555 2.16 LINK NE2 HIS A 212 MN MN A 269 1555 1555 2.15 LINK MN MN A 269 O3B UDP A 270 1555 1555 2.15 LINK MN MN A 269 O2A UDP A 270 1555 1555 2.17 LINK OD2 ASP B 102 MN MN B 269 1555 1555 2.04 LINK OD1 ASP B 104 MN MN B 269 1555 1555 2.08 LINK OD2 ASP B 104 MN MN B 269 1555 1555 2.18 LINK NE2 HIS B 212 MN MN B 269 1555 1555 2.16 LINK MN MN B 269 O1B UDP B 270 1555 1555 2.16 LINK MN MN B 269 O2A UDP B 270 1555 1555 2.21 CISPEP 1 GLU A 119 LEU A 120 0 -7.07 CISPEP 2 GLU B 119 LEU B 120 0 -6.73 CRYST1 46.679 46.739 69.690 79.56 88.71 76.86 P 1 2 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 0.021423 -0.005001 0.000429 0.00000 SCALE2 0.000000 0.021971 -0.004040 0.00000 SCALE3 0.000000 0.000000 0.014594 0.00000