HEADER TRANSFERASE 08-OCT-14 4WLZ TITLE CRYSTAL STRUCTURE OF MOUSE XYLOSIDE XYLOSYLTRANSFERASE 1 COMPLEXED TITLE 2 WITH MANGANESE AND UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSIDE XYLOSYLTRANSFERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UDP-XYLOSE:ALPHA-XYLOSIDE ALPHA-1,3-XYLOSYLTRANSFERASE; COMPND 5 EC: 2.4.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: XXYLT1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.YU,H.LI REVDAT 3 27-DEC-23 4WLZ 1 REMARK LINK REVDAT 2 20-APR-16 4WLZ 1 JRNL REVDAT 1 04-NOV-15 4WLZ 0 JRNL AUTH H.YU,M.TAKEUCHI,J.LEBARRON,J.KANTHARIA,E.LONDON,H.BAKKER, JRNL AUTH 2 R.S.HALTIWANGER,H.LI,H.TAKEUCHI JRNL TITL NOTCH-MODIFYING XYLOSYLTRANSFERASE STRUCTURES SUPPORT AN JRNL TITL 2 SNI-LIKE RETAINING MECHANISM. JRNL REF NAT.CHEM.BIOL. V. 11 847 2015 JRNL REFN ESSN 1552-4469 JRNL PMID 26414444 JRNL DOI 10.1038/NCHEMBIO.1927 REMARK 2 REMARK 2 RESOLUTION. 3.03 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) : 3.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 13780 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 726 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) : 3.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.11 REMARK 3 REFLECTION IN BIN (WORKING SET) : 942 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : 1.89000 REMARK 3 B33 (A**2) : -2.84000 REMARK 3 B12 (A**2) : 0.95000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.525 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4950 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6716 ; 0.962 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 571 ; 4.672 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;33.516 ;23.306 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 818 ;15.816 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.535 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 706 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3786 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4WLZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000204028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14615 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.030 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM HEPES, 1.5 M LI2SO4, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.66233 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 103.32467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 103.32467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.66233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 44.83100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -77.64957 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 51.66233 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 87 REMARK 465 LEU A 88 REMARK 465 GLU A 89 REMARK 465 GLY A 90 REMARK 465 GLY A 91 REMARK 465 VAL A 92 REMARK 465 VAL A 93 REMARK 465 VAL A 94 REMARK 465 PRO A 159 REMARK 465 PRO A 160 REMARK 465 ALA A 161 REMARK 465 ALA A 162 REMARK 465 GLY A 163 REMARK 465 GLY A 194 REMARK 465 SER A 195 REMARK 465 GLY A 196 REMARK 465 THR A 197 REMARK 465 PRO A 390 REMARK 465 GLU A 391 REMARK 465 ASP A 392 REMARK 465 SER B 87 REMARK 465 LEU B 88 REMARK 465 GLU B 89 REMARK 465 GLY B 90 REMARK 465 GLY B 91 REMARK 465 VAL B 92 REMARK 465 VAL B 93 REMARK 465 VAL B 94 REMARK 465 PRO B 95 REMARK 465 PRO B 159 REMARK 465 PRO B 160 REMARK 465 ALA B 161 REMARK 465 ALA B 162 REMARK 465 GLY B 163 REMARK 465 GLU B 391 REMARK 465 ASP B 392 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 353 O PHE A 372 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 144 -38.64 -35.06 REMARK 500 ASP A 201 31.90 -97.16 REMARK 500 ASP A 227 31.09 -97.38 REMARK 500 PRO A 258 33.29 -77.90 REMARK 500 ASN A 352 88.74 -169.97 REMARK 500 PHE B 104 59.15 -146.01 REMARK 500 LYS B 189 -35.19 -36.17 REMARK 500 SER B 195 -31.54 -36.29 REMARK 500 ASP B 201 35.68 -86.00 REMARK 500 MET B 256 37.69 -96.36 REMARK 500 PRO B 258 42.05 -74.92 REMARK 500 ASN B 352 63.57 -151.07 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 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 225 OD2 REMARK 620 2 ASP A 227 OD1 94.7 REMARK 620 3 ASP A 227 OD2 148.8 54.5 REMARK 620 4 HIS A 382 NE2 90.2 84.3 82.5 REMARK 620 5 UDP A 402 O1B 110.4 154.9 100.5 94.3 REMARK 620 6 UDP A 402 O1A 104.0 78.3 76.8 158.2 96.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 225 OD2 REMARK 620 2 ASP B 227 OD1 94.1 REMARK 620 3 ASP B 227 OD2 146.4 53.4 REMARK 620 4 HIS B 382 NE2 92.6 90.5 80.7 REMARK 620 5 UDP B 402 O2A 98.1 76.7 83.7 163.9 REMARK 620 6 UDP B 402 O3B 126.7 126.6 84.8 116.6 65.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WLG RELATED DB: PDB REMARK 900 RELATED ID: 4WLM RELATED DB: PDB REMARK 900 RELATED ID: 4WM0 RELATED DB: PDB REMARK 900 RELATED ID: 4WMA RELATED DB: PDB REMARK 900 RELATED ID: 4WMB RELATED DB: PDB DBREF 4WLZ A 87 392 UNP Q3U4G3 XXLT1_MOUSE 87 392 DBREF 4WLZ B 87 392 UNP Q3U4G3 XXLT1_MOUSE 87 392 SEQRES 1 A 306 SER LEU GLU GLY GLY VAL VAL VAL PRO VAL ASP TYR HIS SEQRES 2 A 306 LEU LEU MET MET PHE THR LYS ALA GLU HIS ASN ALA PRO SEQRES 3 A 306 LEU GLN ALA LYS ALA ARG VAL ALA LEU SER SER LEU LEU SEQRES 4 A 306 ARG LEU ALA LYS PHE GLU ALA HIS GLU VAL LEU ASN LEU SEQRES 5 A 306 HIS PHE VAL SER GLU GLU ALA SER ARG GLU VAL ALA LYS SEQRES 6 A 306 ALA LEU LEU ARG GLU LEU LEU PRO PRO ALA ALA GLY PHE SEQRES 7 A 306 LYS CYS LYS VAL ILE PHE HIS ASP VAL ALA VAL LEU THR SEQRES 8 A 306 ASP LYS LEU PHE PRO VAL VAL GLU ALA MET GLN LYS TYR SEQRES 9 A 306 PHE SER ALA GLY SER GLY THR TYR TYR SER ASP SER ILE SEQRES 10 A 306 PHE PHE LEU SER VAL ALA MET HIS GLN ILE MET PRO LYS SEQRES 11 A 306 GLU ILE PRO ARG ILE ILE GLN LEU ASP LEU ASP LEU LYS SEQRES 12 A 306 TYR LYS THR ASN ILE ARG GLU LEU PHE GLU GLU PHE ASP SEQRES 13 A 306 ASN PHE LEU PRO GLY ALA VAL ILE GLY ILE ALA ARG GLU SEQRES 14 A 306 MET GLN PRO VAL TYR ARG HIS THR PHE TRP GLN PHE ARG SEQRES 15 A 306 HIS GLU ASN PRO LYS THR ARG VAL GLY ASP PRO PRO PRO SEQRES 16 A 306 GLU GLY LEU PRO GLY PHE ASN SER GLY VAL MET LEU LEU SEQRES 17 A 306 ASN LEU GLU ALA MET ARG GLN SER PRO LEU TYR SER HIS SEQRES 18 A 306 LEU LEU GLU PRO SER TRP VAL GLN GLN LEU ALA ASP LYS SEQRES 19 A 306 TYR HIS PHE ARG GLY HIS LEU GLY ASP GLN ASP PHE PHE SEQRES 20 A 306 THR MET ILE GLY MET GLU HIS PRO GLU LEU PHE HIS VAL SEQRES 21 A 306 LEU ASP CYS THR TRP ASN ARG GLN LEU CYS THR TRP TRP SEQRES 22 A 306 ARG ASP HIS GLY TYR SER ASP VAL PHE GLN ALA TYR PHE SEQRES 23 A 306 ARG CYS GLU GLY HIS VAL LYS ILE TYR HIS GLY ASN CYS SEQRES 24 A 306 ASN THR PRO ILE PRO GLU ASP SEQRES 1 B 306 SER LEU GLU GLY GLY VAL VAL VAL PRO VAL ASP TYR HIS SEQRES 2 B 306 LEU LEU MET MET PHE THR LYS ALA GLU HIS ASN ALA PRO SEQRES 3 B 306 LEU GLN ALA LYS ALA ARG VAL ALA LEU SER SER LEU LEU SEQRES 4 B 306 ARG LEU ALA LYS PHE GLU ALA HIS GLU VAL LEU ASN LEU SEQRES 5 B 306 HIS PHE VAL SER GLU GLU ALA SER ARG GLU VAL ALA LYS SEQRES 6 B 306 ALA LEU LEU ARG GLU LEU LEU PRO PRO ALA ALA GLY PHE SEQRES 7 B 306 LYS CYS LYS VAL ILE PHE HIS ASP VAL ALA VAL LEU THR SEQRES 8 B 306 ASP LYS LEU PHE PRO VAL VAL GLU ALA MET GLN LYS TYR SEQRES 9 B 306 PHE SER ALA GLY SER GLY THR TYR TYR SER ASP SER ILE SEQRES 10 B 306 PHE PHE LEU SER VAL ALA MET HIS GLN ILE MET PRO LYS SEQRES 11 B 306 GLU ILE PRO ARG ILE ILE GLN LEU ASP LEU ASP LEU LYS SEQRES 12 B 306 TYR LYS THR ASN ILE ARG GLU LEU PHE GLU GLU PHE ASP SEQRES 13 B 306 ASN PHE LEU PRO GLY ALA VAL ILE GLY ILE ALA ARG GLU SEQRES 14 B 306 MET GLN PRO VAL TYR ARG HIS THR PHE TRP GLN PHE ARG SEQRES 15 B 306 HIS GLU ASN PRO LYS THR ARG VAL GLY ASP PRO PRO PRO SEQRES 16 B 306 GLU GLY LEU PRO GLY PHE ASN SER GLY VAL MET LEU LEU SEQRES 17 B 306 ASN LEU GLU ALA MET ARG GLN SER PRO LEU TYR SER HIS SEQRES 18 B 306 LEU LEU GLU PRO SER TRP VAL GLN GLN LEU ALA ASP LYS SEQRES 19 B 306 TYR HIS PHE ARG GLY HIS LEU GLY ASP GLN ASP PHE PHE SEQRES 20 B 306 THR MET ILE GLY MET GLU HIS PRO GLU LEU PHE HIS VAL SEQRES 21 B 306 LEU ASP CYS THR TRP ASN ARG GLN LEU CYS THR TRP TRP SEQRES 22 B 306 ARG ASP HIS GLY TYR SER ASP VAL PHE GLN ALA TYR PHE SEQRES 23 B 306 ARG CYS GLU GLY HIS VAL LYS ILE TYR HIS GLY ASN CYS SEQRES 24 B 306 ASN THR PRO ILE PRO GLU ASP HET MN A 401 1 HET UDP A 402 25 HET SO4 A 403 5 HET MN B 401 1 HET UDP B 402 25 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 5 SO4 O4 S 2- HELIX 1 AA1 ASN A 110 ALA A 128 1 19 HELIX 2 AA2 GLU A 143 ARG A 155 1 13 HELIX 3 AA3 VAL A 173 GLU A 185 1 13 HELIX 4 AA4 ALA A 186 GLN A 188 5 3 HELIX 5 AA5 TYR A 199 VAL A 208 5 10 HELIX 6 AA6 ALA A 209 MET A 214 1 6 HELIX 7 AA7 ILE A 234 GLU A 239 1 6 HELIX 8 AA8 GLU A 240 ASP A 242 5 3 HELIX 9 AA9 PRO A 258 PHE A 264 1 7 HELIX 10 AB1 PHE A 264 ASN A 271 1 8 HELIX 11 AB2 ASN A 295 SER A 302 1 8 HELIX 12 AB3 SER A 302 LEU A 309 1 8 HELIX 13 AB4 GLU A 310 HIS A 322 1 13 HELIX 14 AB5 GLY A 328 HIS A 340 1 13 HELIX 15 AB6 ASP A 348 ASN A 352 5 5 HELIX 16 AB7 THR A 357 HIS A 362 5 6 HELIX 17 AB8 VAL A 367 ARG A 373 1 7 HELIX 18 AB9 ASN A 384 THR A 387 5 4 HELIX 19 AC1 ASN B 110 ARG B 126 1 17 HELIX 20 AC2 GLU B 143 GLU B 156 1 14 HELIX 21 AC3 ASP B 172 GLU B 185 1 14 HELIX 22 AC4 MET B 187 PHE B 191 5 5 HELIX 23 AC5 GLY B 194 TYR B 198 5 5 HELIX 24 AC6 TYR B 199 LEU B 206 5 8 HELIX 25 AC7 ALA B 209 MET B 214 1 6 HELIX 26 AC8 ASN B 233 PHE B 244 5 12 HELIX 27 AC9 PRO B 258 PHE B 264 1 7 HELIX 28 AD1 PHE B 264 ASN B 271 1 8 HELIX 29 AD2 LEU B 296 SER B 302 1 7 HELIX 30 AD3 SER B 302 LEU B 308 1 7 HELIX 31 AD4 GLU B 310 HIS B 322 1 13 HELIX 32 AD5 GLY B 328 HIS B 340 1 13 HELIX 33 AD6 ASP B 348 ASN B 352 5 5 HELIX 34 AD7 TRP B 359 GLY B 363 5 5 HELIX 35 AD8 VAL B 367 ARG B 373 1 7 SHEET 1 AA1 7 LYS A 165 ASP A 172 0 SHEET 2 AA1 7 VAL A 135 SER A 142 1 N PHE A 140 O HIS A 171 SHEET 3 AA1 7 ASP A 97 MET A 103 1 N TYR A 98 O ASN A 137 SHEET 4 AA1 7 ILE A 221 LEU A 224 1 O LEU A 224 N LEU A 101 SHEET 5 AA1 7 PHE A 287 LEU A 294 -1 O LEU A 294 N ILE A 221 SHEET 6 AA1 7 ILE A 250 ARG A 254 -1 N GLY A 251 O LEU A 293 SHEET 7 AA1 7 PHE A 344 LEU A 347 1 O HIS A 345 N ILE A 250 SHEET 1 AA2 3 LEU A 228 TYR A 230 0 SHEET 2 AA2 3 ILE A 380 HIS A 382 -1 O TYR A 381 N LYS A 229 SHEET 3 AA2 3 ARG A 353 GLN A 354 1 N ARG A 353 O ILE A 380 SHEET 1 AA3 7 ILE B 169 HIS B 171 0 SHEET 2 AA3 7 VAL B 135 VAL B 141 1 N LEU B 138 O ILE B 169 SHEET 3 AA3 7 ASP B 97 MET B 103 1 N TYR B 98 O ASN B 137 SHEET 4 AA3 7 ARG B 220 LEU B 224 1 O LEU B 224 N LEU B 101 SHEET 5 AA3 7 PHE B 287 ASN B 295 -1 O LEU B 294 N ILE B 221 SHEET 6 AA3 7 ILE B 250 ARG B 254 -1 N GLY B 251 O LEU B 293 SHEET 7 AA3 7 PHE B 344 LEU B 347 1 O HIS B 345 N ILE B 250 SHEET 1 AA4 3 LEU B 228 TYR B 230 0 SHEET 2 AA4 3 ILE B 380 HIS B 382 -1 O TYR B 381 N LYS B 229 SHEET 3 AA4 3 ARG B 353 GLN B 354 1 N ARG B 353 O HIS B 382 SSBOND 1 CYS A 349 CYS A 374 1555 1555 2.03 SSBOND 2 CYS A 356 CYS A 385 1555 1555 2.03 SSBOND 3 CYS B 349 CYS B 374 1555 1555 2.04 SSBOND 4 CYS B 356 CYS B 385 1555 1555 2.03 LINK OD2 ASP A 225 MN MN A 401 1555 1555 2.02 LINK OD1 ASP A 227 MN MN A 401 1555 1555 2.35 LINK OD2 ASP A 227 MN MN A 401 1555 1555 2.43 LINK NE2 HIS A 382 MN MN A 401 1555 1555 2.25 LINK MN MN A 401 O1B UDP A 402 1555 1555 2.12 LINK MN MN A 401 O1A UDP A 402 1555 1555 2.34 LINK OD2 ASP B 225 MN MN B 401 1555 1555 2.16 LINK OD1 ASP B 227 MN MN B 401 1555 1555 2.43 LINK OD2 ASP B 227 MN MN B 401 1555 1555 2.43 LINK NE2 HIS B 382 MN MN B 401 1555 1555 2.17 LINK MN MN B 401 O2A UDP B 402 1555 1555 2.31 LINK MN MN B 401 O3B UDP B 402 1555 1555 2.28 CISPEP 1 PRO A 280 PRO A 281 0 2.75 CISPEP 2 PRO B 280 PRO B 281 0 0.42 SITE 1 AC1 4 ASP A 225 ASP A 227 HIS A 382 UDP A 402 SITE 1 AC2 13 MET A 103 PHE A 104 THR A 105 LEU A 113 SITE 2 AC2 13 ASP A 225 LEU A 226 ASP A 227 HIS A 382 SITE 3 AC2 13 ASN A 384 CYS A 385 MN A 401 ASP B 361 SITE 4 AC2 13 HIS B 362 SITE 1 AC3 4 ARG A 261 ARG A 268 TYR A 364 SER B 195 SITE 1 AC4 4 ASP B 225 ASP B 227 HIS B 382 UDP B 402 SITE 1 AC5 14 TRP A 358 ASP A 361 HIS A 362 MET B 103 SITE 2 AC5 14 PHE B 104 THR B 105 LEU B 113 LYS B 116 SITE 3 AC5 14 ASP B 225 LEU B 226 ASP B 227 ASN B 384 SITE 4 AC5 14 CYS B 385 MN B 401 CRYST1 89.662 89.662 154.987 90.00 90.00 120.00 P 31 2 1 12 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 0.011153 0.006439 0.000000 0.00000 SCALE2 0.000000 0.012878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006452 0.00000