HEADER TRANSFERASE 04-OCT-11 3U2X TITLE CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH TITLE 2 MANGANESE, UDP AND 1'-DEOXYGLUCOSE 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: 562; 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 3 13-SEP-23 3U2X 1 HETSYN REVDAT 2 29-JUL-20 3U2X 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE REVDAT 1 02-NOV-11 3U2X 0 JRNL AUTH A.CHAIKUAD,D.S.FROESE,E.KRYSZTOFINSKA,F.VON DELFT,J.WEIGELT, JRNL AUTH 2 C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,U.OPPERMANN,W.W.YUE, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED JRNL TITL 2 WITH MANGANESE, UDP AND 1'-DEOXYGLUCOSE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 47790 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2540 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3400 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.4500 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.5210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4164 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.19000 REMARK 3 B22 (A**2) : 0.78000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : -1.78000 REMARK 3 B13 (A**2) : 0.60000 REMARK 3 B23 (A**2) : 0.75000 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): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.543 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4459 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2943 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6062 ; 1.553 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7178 ; 0.985 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.326 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;37.885 ;24.096 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 700 ;13.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.736 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 701 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4796 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 890 ; 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): 2650 ; 0.750 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1054 ; 0.211 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4319 ; 1.285 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1809 ; 1.961 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1737 ; 2.989 ; 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 : 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): 49.5624 27.4361 16.1160 REMARK 3 T TENSOR REMARK 3 T11: 0.0296 T22: 0.0060 REMARK 3 T33: 0.0499 T12: 0.0045 REMARK 3 T13: -0.0012 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.1018 L22: 1.5373 REMARK 3 L33: 2.7062 L12: 0.4241 REMARK 3 L13: -0.3025 L23: 0.1970 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: -0.0358 S13: -0.0290 REMARK 3 S21: 0.0036 S22: -0.0045 S23: -0.0091 REMARK 3 S31: -0.1058 S32: 0.0384 S33: 0.0020 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): 51.3266 7.5283 11.1671 REMARK 3 T TENSOR REMARK 3 T11: 0.1186 T22: 0.0444 REMARK 3 T33: 0.1379 T12: 0.0082 REMARK 3 T13: 0.0207 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 3.0742 L22: 6.1603 REMARK 3 L33: 3.4158 L12: 1.1332 REMARK 3 L13: 0.4617 L23: 0.6785 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: -0.2135 S13: -0.1740 REMARK 3 S21: 0.2348 S22: -0.0699 S23: -0.1058 REMARK 3 S31: 0.5301 S32: 0.0520 S33: 0.0273 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): 38.3248 18.5008 47.3336 REMARK 3 T TENSOR REMARK 3 T11: 0.0131 T22: 0.0216 REMARK 3 T33: 0.0453 T12: 0.0107 REMARK 3 T13: 0.0097 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.4593 L22: 1.0327 REMARK 3 L33: 2.5916 L12: 0.3694 REMARK 3 L13: 0.1810 L23: -0.5184 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: 0.0317 S13: 0.0035 REMARK 3 S21: -0.0416 S22: 0.0170 S23: 0.0239 REMARK 3 S31: 0.0162 S32: -0.1097 S33: -0.0028 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): 57.3839 12.0915 51.9844 REMARK 3 T TENSOR REMARK 3 T11: 0.0580 T22: 0.1420 REMARK 3 T33: 0.1252 T12: 0.0484 REMARK 3 T13: 0.0064 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 6.2653 L22: 2.7477 REMARK 3 L33: 4.0153 L12: 0.0382 REMARK 3 L13: 0.9563 L23: 0.3029 REMARK 3 S TENSOR REMARK 3 S11: -0.0397 S12: 0.3548 S13: -0.2234 REMARK 3 S21: -0.1729 S22: -0.1159 S23: -0.1593 REMARK 3 S31: 0.2525 S32: 0.7010 S33: 0.1556 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 3U2X 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_1000068238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-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 : 50332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 30.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 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 (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M TRI-SODIUM CITRATE DIHYDRATE, 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: 7380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 HIS A 236 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 0 OG REMARK 470 MET B 1 CG SD CE 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 299 O HOH B 462 2.02 REMARK 500 O HOH B 440 O HOH B 472 2.15 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. = 5.9 DEGREES REMARK 500 ASP B 104 OD1 - CG - OD2 ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP B 104 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP B 104 CB - CG - OD2 ANGL. DEV. = 6.8 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 PHE A 171 54.68 -99.43 REMARK 500 ASP A 178 97.64 36.07 REMARK 500 ASN A 188 71.22 -164.09 REMARK 500 PHE B 171 57.54 -102.44 REMARK 500 ASP B 178 100.71 15.08 REMARK 500 ASN B 188 67.24 -160.90 REMARK 500 LYS B 229 49.41 71.04 REMARK 500 ALA B 235 -135.41 53.36 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 97.1 REMARK 620 3 ASP A 104 OD2 152.4 55.4 REMARK 620 4 HIS A 212 NE2 98.1 94.6 88.4 REMARK 620 5 UDP A 264 O1B 100.7 159.8 105.9 92.1 REMARK 620 6 UDP A 264 O1A 91.6 88.2 84.9 169.5 82.0 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 94.2 REMARK 620 3 ASP B 104 OD2 153.4 59.6 REMARK 620 4 HIS B 212 NE2 94.8 92.9 91.1 REMARK 620 5 UDP B 264 O3B 99.8 163.8 105.7 94.1 REMARK 620 6 UDP B 264 O2A 92.8 86.1 81.9 172.4 85.0 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: 3U2W RELATED DB: PDB DBREF 3U2X A 1 262 UNP P46976 GLYG_HUMAN 1 262 DBREF 3U2X B 1 262 UNP P46976 GLYG_HUMAN 1 262 SEQADV 3U2X SER A 0 UNP P46976 EXPRESSION TAG SEQADV 3U2X 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 MN A 263 1 HET UDP A 264 25 HET ASO A 265 22 HET EDO A 266 4 HET EDO A 267 4 HET EDO A 268 4 HET EDO A 269 4 HET EDO A 270 8 HET EDO A 271 4 HET EDO A 272 4 HET EDO A 273 4 HET MN B 263 1 HET UDP B 264 25 HET ASO B 265 22 HET EDO B 266 4 HET EDO B 267 4 HET EDO B 268 4 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM ASO 1,5-ANHYDRO-D-GLUCITOL HETNAM EDO 1,2-ETHANEDIOL HETSYN ASO 1,5-ANHYDROSORBITOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MN 2(MN 2+) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 5 ASO 2(C6 H12 O5) FORMUL 6 EDO 11(C2 H6 O2) FORMUL 20 HOH *421(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 GLN A 156 1 15 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 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 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 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 ARG B 34 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 TYR B 139 N CYS B 98 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 VAL B 210 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 OD2 ASP A 102 MN MN A 263 1555 1555 2.04 LINK OD1 ASP A 104 MN MN A 263 1555 1555 2.03 LINK OD2 ASP A 104 MN MN A 263 1555 1555 2.49 LINK NE2 HIS A 212 MN MN A 263 1555 1555 2.14 LINK MN MN A 263 O1B UDP A 264 1555 1555 1.99 LINK MN MN A 263 O1A UDP A 264 1555 1555 2.03 LINK OD2 ASP B 102 MN MN B 263 1555 1555 1.99 LINK OD1 ASP B 104 MN MN B 263 1555 1555 2.03 LINK OD2 ASP B 104 MN MN B 263 1555 1555 2.06 LINK NE2 HIS B 212 MN MN B 263 1555 1555 2.14 LINK MN MN B 263 O3B UDP B 264 1555 1555 2.01 LINK MN MN B 263 O2A UDP B 264 1555 1555 2.02 CISPEP 1 GLU A 119 LEU A 120 0 -9.44 CISPEP 2 GLU B 119 LEU B 120 0 -11.11 CRYST1 46.700 46.860 69.700 79.57 88.96 77.25 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 0.021413 -0.004845 0.000499 0.00000 SCALE2 0.000000 0.021880 -0.004039 0.00000 SCALE3 0.000000 0.000000 0.014592 0.00000