HEADER TRANSFERASE 30-NOV-18 6IBO TITLE CATALYTIC DEFICIENCY OF O-GLCNAC TRANSFERASE LEADS TO X-LINKED TITLE 2 INTELLECTUAL DISABILITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N- COMPND 3 ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: O-GLCNAC TRANSFERASE SUBUNIT P110,O-LINKED N- COMPND 6 ACETYLGLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT; COMPND 7 EC: 2.4.1.255; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ALA-VAL-SER-ARG-ALA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: KKVAVSRA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: OGT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GUNDOGDU,D.M.F.VAN AALTEN REVDAT 3 24-JAN-24 6IBO 1 REMARK REVDAT 2 31-JUL-19 6IBO 1 JRNL REVDAT 1 24-JUL-19 6IBO 0 JRNL AUTH V.M.PRAVATA,V.MUHA,M.GUNDOGDU,A.T.FERENBACH,P.S.KAKADE, JRNL AUTH 2 V.VANDADI,A.C.WILMES,V.S.BORODKIN,S.JOSS,M.P.STAVRIDIS, JRNL AUTH 3 D.M.F.VAN AALTEN JRNL TITL CATALYTIC DEFICIENCY OF O-GLCNAC TRANSFERASE LEADS TO JRNL TITL 2 X-LINKED INTELLECTUAL DISABILITY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 14961 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31296563 JRNL DOI 10.1073/PNAS.1900065116 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 51399 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2677 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) : 2.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3803 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3500 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5528 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.93000 REMARK 3 B22 (A**2) : 4.70000 REMARK 3 B33 (A**2) : -2.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.002 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 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): 5702 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5254 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7737 ; 1.781 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12228 ; 1.060 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 696 ; 6.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;41.025 ;24.483 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 979 ;15.798 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 859 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6268 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1097 ; 0.002 ; 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): 2797 ; 4.955 ; 5.344 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2798 ; 4.954 ; 5.345 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3490 ; 6.760 ; 7.994 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3490 ; 6.760 ; 7.994 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2902 ; 5.296 ; 5.794 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2895 ; 5.169 ; 5.791 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4236 ; 7.685 ; 8.485 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6405 ; 9.782 ;62.699 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6352 ; 9.763 ;62.603 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6IBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99187 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 286887 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.91000 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5C1D REMARK 200 REMARK 200 REMARK: LARGE AND AMORPHOUS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.45 M K2HPO4, 8 MM EDTA AND 1% REMARK 280 XYLITOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.30850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 99.99800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.30850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 99.99800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 75.30850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 99.99800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 75.30850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 99.99800 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 99.99800 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 99.99800 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 99.99800 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 99.99800 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 75.30850 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 75.30850 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 75.30850 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 68.86850 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 75.30850 REMARK 290 SMTRY3 16 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 A1344 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 GLY A 319 REMARK 465 PRO A 320 REMARK 465 GLY A 321 REMARK 465 SER A 322 REMARK 465 CYS A 323 REMARK 465 PRO A 324 REMARK 465 ASN A 726 REMARK 465 GLY A 727 REMARK 465 HIS A 728 REMARK 465 LYS A 757 REMARK 465 CYS A 758 REMARK 465 PRO A 759 REMARK 465 ASP A 760 REMARK 465 GLY A 761 REMARK 465 GLY A 762 REMARK 465 ASP A 763 REMARK 465 ASN A 764 REMARK 465 ALA A 765 REMARK 465 ASP A 766 REMARK 465 SER A 767 REMARK 465 SER A 768 REMARK 465 ASN A 769 REMARK 465 THR A 770 REMARK 465 ALA A 771 REMARK 465 LYS A 1038 REMARK 465 PRO A 1039 REMARK 465 VAL A 1040 REMARK 465 GLU A 1041 REMARK 465 LYS C 0 REMARK 465 LYS C 1 REMARK 465 VAL C 2 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 ALA C 8 CA C O CB 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 A 1329 O HOH A 1404 1.18 REMARK 500 O HOH A 1243 O HOH A 1424 1.37 REMARK 500 SD MET A 674 O HOH A 1426 1.66 REMARK 500 O HOH A 1201 O HOH A 1400 1.72 REMARK 500 OG1 THR A 1009 O HOH A 1201 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 630 OE1 GLN A 630 11454 1.62 REMARK 500 O HOH A 1436 O HOH A 1436 8554 1.71 REMARK 500 OG SER A 329 OG SER A 329 2565 2.09 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 ARG A 453 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 453 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 526 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 914 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A1001 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A1001 NE - CZ - NH2 ANGL. DEV. = -4.4 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 GLU A 359 38.13 -78.35 REMARK 500 ASN A 444 75.52 -106.77 REMARK 500 THR A 480 117.31 -37.03 REMARK 500 HIS A 539 61.84 62.70 REMARK 500 PRO A 546 131.51 -39.79 REMARK 500 SER A 552 43.39 -105.74 REMARK 500 ASP A 553 33.26 34.20 REMARK 500 ILE A 618 76.31 -118.89 REMARK 500 TYR A 642 58.37 -93.96 REMARK 500 ARG A 654 64.87 38.68 REMARK 500 LEU A 663 -53.47 82.65 REMARK 500 THR A 679 -151.86 -154.87 REMARK 500 HIS A 701 -92.44 -114.34 REMARK 500 LYS A 724 -82.32 -119.16 REMARK 500 ASN A 732 33.02 -142.62 REMARK 500 MET A 779 62.00 -67.30 REMARK 500 ASN A 814 100.10 -167.19 REMARK 500 ASN A 870 -43.88 74.80 REMARK 500 ASN A 898 -5.13 -38.62 REMARK 500 HIS A 930 -90.61 -105.46 REMARK 500 ASP A 986 78.84 -67.77 REMARK 500 PRO A1033 123.66 -38.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1510 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1511 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A1512 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A1513 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A1514 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A1515 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A1516 DISTANCE = 8.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 12V A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 1103 DBREF 6IBO A 323 1041 UNP O15294 OGT1_HUMAN 323 1041 DBREF 6IBO C 0 8 PDB 6IBO 6IBO 0 8 SEQADV 6IBO GLY A 319 UNP O15294 EXPRESSION TAG SEQADV 6IBO PRO A 320 UNP O15294 EXPRESSION TAG SEQADV 6IBO GLY A 321 UNP O15294 EXPRESSION TAG SEQADV 6IBO SER A 322 UNP O15294 EXPRESSION TAG SEQADV 6IBO LYS A 567 UNP O15294 ASN 567 CONFLICT SEQRES 1 A 723 GLY PRO GLY SER CYS PRO THR HIS ALA ASP SER LEU ASN SEQRES 2 A 723 ASN LEU ALA ASN ILE LYS ARG GLU GLN GLY ASN ILE GLU SEQRES 3 A 723 GLU ALA VAL ARG LEU TYR ARG LYS ALA LEU GLU VAL PHE SEQRES 4 A 723 PRO GLU PHE ALA ALA ALA HIS SER ASN LEU ALA SER VAL SEQRES 5 A 723 LEU GLN GLN GLN GLY LYS LEU GLN GLU ALA LEU MET HIS SEQRES 6 A 723 TYR LYS GLU ALA ILE ARG ILE SER PRO THR PHE ALA ASP SEQRES 7 A 723 ALA TYR SER ASN MET GLY ASN THR LEU LYS GLU MET GLN SEQRES 8 A 723 ASP VAL GLN GLY ALA LEU GLN CYS TYR THR ARG ALA ILE SEQRES 9 A 723 GLN ILE ASN PRO ALA PHE ALA ASP ALA HIS SER ASN LEU SEQRES 10 A 723 ALA SER ILE HIS LYS ASP SER GLY ASN ILE PRO GLU ALA SEQRES 11 A 723 ILE ALA SER TYR ARG THR ALA LEU LYS LEU LYS PRO ASP SEQRES 12 A 723 PHE PRO ASP ALA TYR CYS ASN LEU ALA HIS CYS LEU GLN SEQRES 13 A 723 ILE VAL CYS ASP TRP THR ASP TYR ASP GLU ARG MET LYS SEQRES 14 A 723 LYS LEU VAL SER ILE VAL ALA ASP GLN LEU GLU LYS ASN SEQRES 15 A 723 ARG LEU PRO SER VAL HIS PRO HIS HIS SER MET LEU TYR SEQRES 16 A 723 PRO LEU SER HIS GLY PHE ARG LYS ALA ILE ALA GLU ARG SEQRES 17 A 723 HIS GLY ASN LEU CYS LEU ASP LYS ILE ASN VAL LEU HIS SEQRES 18 A 723 LYS PRO PRO TYR GLU HIS PRO LYS ASP LEU LYS LEU SER SEQRES 19 A 723 ASP GLY ARG LEU ARG VAL GLY TYR VAL SER SER ASP PHE SEQRES 20 A 723 GLY LYS HIS PRO THR SER HIS LEU MET GLN SER ILE PRO SEQRES 21 A 723 GLY MET HIS ASN PRO ASP LYS PHE GLU VAL PHE CYS TYR SEQRES 22 A 723 ALA LEU SER PRO ASP ASP GLY THR ASN PHE ARG VAL LYS SEQRES 23 A 723 VAL MET ALA GLU ALA ASN HIS PHE ILE ASP LEU SER GLN SEQRES 24 A 723 ILE PRO CYS ASN GLY LYS ALA ALA ASP ARG ILE HIS GLN SEQRES 25 A 723 ASP GLY ILE HIS ILE LEU VAL ASN MET ASN GLY TYR THR SEQRES 26 A 723 LYS GLY ALA ARG ASN GLU LEU PHE ALA LEU ARG PRO ALA SEQRES 27 A 723 PRO ILE GLN ALA MET TRP LEU GLY TYR PRO GLY THR SER SEQRES 28 A 723 GLY ALA LEU PHE MET ASP TYR ILE ILE THR ASP GLN GLU SEQRES 29 A 723 THR SER PRO ALA GLU VAL ALA GLU GLN TYR SER GLU LYS SEQRES 30 A 723 LEU ALA TYR MET PRO HIS THR PHE PHE ILE GLY ASP HIS SEQRES 31 A 723 ALA ASN MET PHE PRO HIS LEU LYS LYS LYS ALA VAL ILE SEQRES 32 A 723 ASP PHE LYS SER ASN GLY HIS ILE TYR ASP ASN ARG ILE SEQRES 33 A 723 VAL LEU ASN GLY ILE ASP LEU LYS ALA PHE LEU ASP SER SEQRES 34 A 723 LEU PRO ASP VAL LYS ILE VAL LYS MET LYS CYS PRO ASP SEQRES 35 A 723 GLY GLY ASP ASN ALA ASP SER SER ASN THR ALA LEU ASN SEQRES 36 A 723 MET PRO VAL ILE PRO MET ASN THR ILE ALA GLU ALA VAL SEQRES 37 A 723 ILE GLU MET ILE ASN ARG GLY GLN ILE GLN ILE THR ILE SEQRES 38 A 723 ASN GLY PHE SER ILE SER ASN GLY LEU ALA THR THR GLN SEQRES 39 A 723 ILE ASN ASN LYS ALA ALA THR GLY GLU GLU VAL PRO ARG SEQRES 40 A 723 THR ILE ILE VAL THR THR ARG SER GLN TYR GLY LEU PRO SEQRES 41 A 723 GLU ASP ALA ILE VAL TYR CYS ASN PHE ASN GLN LEU TYR SEQRES 42 A 723 LYS ILE ASP PRO SER THR LEU GLN MET TRP ALA ASN ILE SEQRES 43 A 723 LEU LYS ARG VAL PRO ASN SER VAL LEU TRP LEU LEU ARG SEQRES 44 A 723 PHE PRO ALA VAL GLY GLU PRO ASN ILE GLN GLN TYR ALA SEQRES 45 A 723 GLN ASN MET GLY LEU PRO GLN ASN ARG ILE ILE PHE SER SEQRES 46 A 723 PRO VAL ALA PRO LYS GLU GLU HIS VAL ARG ARG GLY GLN SEQRES 47 A 723 LEU ALA ASP VAL CYS LEU ASP THR PRO LEU CYS ASN GLY SEQRES 48 A 723 HIS THR THR GLY MET ASP VAL LEU TRP ALA GLY THR PRO SEQRES 49 A 723 MET VAL THR MET PRO GLY GLU THR LEU ALA SER ARG VAL SEQRES 50 A 723 ALA ALA SER GLN LEU THR CYS LEU GLY CYS LEU GLU LEU SEQRES 51 A 723 ILE ALA LYS ASN ARG GLN GLU TYR GLU ASP ILE ALA VAL SEQRES 52 A 723 LYS LEU GLY THR ASP LEU GLU TYR LEU LYS LYS VAL ARG SEQRES 53 A 723 GLY LYS VAL TRP LYS GLN ARG ILE SER SER PRO LEU PHE SEQRES 54 A 723 ASN THR LYS GLN TYR THR MET GLU LEU GLU ARG LEU TYR SEQRES 55 A 723 LEU GLN MET TRP GLU HIS TYR ALA ALA GLY ASN LYS PRO SEQRES 56 A 723 ASP HIS MET ILE LYS PRO VAL GLU SEQRES 1 C 9 LYS LYS VAL ALA VAL SER ARG ALA ALA HET 12V A1101 39 HET PO4 A1102 5 HET PO4 A1103 5 HETNAM 12V (2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6- HETNAM 2 12V (HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S, HETNAM 3 12V 4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3, HETNAM 4 12V 4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN HETNAM 5 12V DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETSYN 12V URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE FORMUL 3 12V C17 H27 N3 O16 P2 S FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 HOH *318(H2 O) HELIX 1 AA1 THR A 325 GLN A 340 1 16 HELIX 2 AA2 ASN A 342 PHE A 357 1 16 HELIX 3 AA3 PHE A 360 GLN A 374 1 15 HELIX 4 AA4 LYS A 376 SER A 391 1 16 HELIX 5 AA5 PHE A 394 MET A 408 1 15 HELIX 6 AA6 ASP A 410 ASN A 425 1 16 HELIX 7 AA7 PHE A 428 SER A 442 1 15 HELIX 8 AA8 ASN A 444 LYS A 459 1 16 HELIX 9 AA9 PHE A 462 VAL A 476 1 15 HELIX 10 AB1 ASP A 481 LYS A 499 1 19 HELIX 11 AB2 HIS A 506 TYR A 513 5 8 HELIX 12 AB3 SER A 516 VAL A 537 1 22 HELIX 13 AB4 LEU A 549 ASP A 553 5 5 HELIX 14 AB5 HIS A 568 GLN A 575 1 8 HELIX 15 AB6 SER A 576 HIS A 581 1 6 HELIX 16 AB7 THR A 599 ALA A 609 1 11 HELIX 17 AB8 SER A 616 ILE A 618 5 3 HELIX 18 AB9 CYS A 620 GLY A 632 1 13 HELIX 19 AC1 ASN A 648 LEU A 653 1 6 HELIX 20 AC2 PRO A 685 TYR A 692 5 8 HELIX 21 AC3 ASP A 707 PHE A 712 1 6 HELIX 22 AC4 PRO A 713 LYS A 716 5 4 HELIX 23 AC5 ASP A 740 SER A 747 1 8 HELIX 24 AC6 ASN A 780 ARG A 792 1 13 HELIX 25 AC7 ALA A 809 ASN A 814 1 6 HELIX 26 AC8 ASN A 814 THR A 819 1 6 HELIX 27 AC9 SER A 833 GLY A 836 5 4 HELIX 28 AD1 GLN A 849 ILE A 853 5 5 HELIX 29 AD2 ASP A 854 VAL A 868 1 15 HELIX 30 AD3 PRO A 879 VAL A 881 5 3 HELIX 31 AD4 GLY A 882 GLY A 894 1 13 HELIX 32 AD5 PRO A 896 ASN A 898 5 3 HELIX 33 AD6 PRO A 907 GLN A 916 1 10 HELIX 34 AD7 HIS A 930 ALA A 939 1 10 HELIX 35 AD8 THR A 950 SER A 953 5 4 HELIX 36 AD9 ARG A 954 GLY A 964 1 11 HELIX 37 AE1 CYS A 965 ILE A 969 5 5 HELIX 38 AE2 ASN A 972 ASP A 986 1 15 HELIX 39 AE3 ASP A 986 SER A 1004 1 19 HELIX 40 AE4 ASN A 1008 ALA A 1029 1 22 SHEET 1 AA1 7 HIS A 611 ASP A 614 0 SHEET 2 AA1 7 PHE A 586 ALA A 592 1 N CYS A 590 O ILE A 613 SHEET 3 AA1 7 LEU A 556 SER A 562 1 N TYR A 560 O TYR A 591 SHEET 4 AA1 7 ILE A 635 ASN A 638 1 O VAL A 637 N GLY A 559 SHEET 5 AA1 7 ILE A 658 MET A 661 1 O ALA A 660 N ASN A 638 SHEET 6 AA1 7 TYR A 676 THR A 679 1 O ILE A 678 N MET A 661 SHEET 7 AA1 7 LYS A 695 TYR A 698 1 O ALA A 697 N THR A 679 SHEET 1 AA2 7 LYS A 752 VAL A 754 0 SHEET 2 AA2 7 MET A 774 ILE A 777 -1 O VAL A 776 N LYS A 752 SHEET 3 AA2 7 ALA A 719 ILE A 721 1 N VAL A 720 O ILE A 777 SHEET 4 AA2 7 ILE A 734 ASN A 737 -1 O LEU A 736 N ALA A 719 SHEET 5 AA2 7 ILE A 827 THR A 831 -1 O THR A 830 N VAL A 735 SHEET 6 AA2 7 PHE A 802 ASN A 806 1 N SER A 805 O ILE A 827 SHEET 7 AA2 7 GLN A 796 ILE A 799 -1 N ILE A 797 O ILE A 804 SHEET 1 AA3 5 ILE A 900 PRO A 904 0 SHEET 2 AA3 5 VAL A 872 ARG A 877 1 N ARG A 877 O SER A 903 SHEET 3 AA3 5 VAL A 843 ASN A 846 1 N TYR A 844 O TRP A 874 SHEET 4 AA3 5 VAL A 920 LEU A 922 1 O LEU A 922 N CYS A 845 SHEET 5 AA3 5 MET A 943 VAL A 944 1 O VAL A 944 N CYS A 921 CISPEP 1 PHE A 878 PRO A 879 0 3.00 SITE 1 AC1 27 HIS A 508 PRO A 569 THR A 570 LEU A 663 SITE 2 AC1 27 GLY A 664 PRO A 666 PHE A 704 GLN A 849 SITE 3 AC1 27 TYR A 851 LYS A 852 VAL A 905 ALA A 906 SITE 4 AC1 27 LYS A 908 HIS A 911 ARG A 914 CYS A 927 SITE 5 AC1 27 HIS A 930 THR A 931 THR A 932 ASP A 935 SITE 6 AC1 27 HOH A1268 HOH A1274 HOH A1310 ALA C 3 SITE 7 AC1 27 VAL C 4 SER C 5 HOH C 101 SITE 1 AC2 5 GLN A 423 PRO A 446 VAL A 476 VAL A 881 SITE 2 AC2 5 ASN A 885 SITE 1 AC3 7 SER A 805 THR A 810 ILE A 813 PRO A 824 SITE 2 AC3 7 THR A 826 ILE A 828 HOH A1362 CRYST1 137.737 150.617 199.996 90.00 90.00 90.00 F 2 2 2 16 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 0.007260 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005000 0.00000