HEADER BIOSYNTHETIC PROTEIN 15-MAY-20 6Z2F TITLE CRYSTAL STRUCTURE OF HUMAN AGX1 MUTANT COMPLEXED WITH UDPGLCNAC CAVEAT 6Z2F UD1 A 601 HAS WRONG CHIRALITY AT ATOM C1' UD1 A 601 HAS CAVEAT 2 6Z2F WRONG CHIRALITY AT ATOM C3' UD1 A 601 HAS WRONG CHIRALITY CAVEAT 3 6Z2F AT ATOM C4' UD1 B 601 HAS WRONG CHIRALITY AT ATOM C3' UD1 B CAVEAT 4 6Z2F 601 HAS WRONG CHIRALITY AT ATOM C4' COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLHEXOSAMINE PYROPHOSPHORYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTIGEN X,AGX,SPERM-ASSOCIATED ANTIGEN 2; COMPND 5 EC: 2.7.7.83,2.7.7.23; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UDP-N-ACETYLHEXOSAMINE PYROPHOSPHORYLASE; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ANTIGEN X,AGX,SPERM-ASSOCIATED ANTIGEN 2; COMPND 11 EC: 2.7.7.83,2.7.7.23; COMPND 12 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: UAP1, SPAG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UAP1, SPAG2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEXOSAMINE BIOSYNTHETIC PATHWAY AGX1 DISEASE MUTANT, BIOSYNTHETIC KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,D.M.F.VAN AALTEN REVDAT 2 24-JAN-24 6Z2F 1 REMARK REVDAT 1 26-MAY-21 6Z2F 0 JRNL AUTH X.CHEN,D.M.F.VAN AALTEN JRNL TITL CRYSTAL STRUCTURE OF HUMAN AGX1 MUTANT COMPLEXED WITH JRNL TITL 2 UDPGLCNAC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 88736 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4676 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6300 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 336 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7535 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 701 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.01000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.59000 REMARK 3 B13 (A**2) : -0.77000 REMARK 3 B23 (A**2) : -0.36000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.641 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7781 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7185 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10519 ; 1.640 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16727 ; 1.039 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 933 ; 5.960 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 376 ;37.143 ;25.080 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1353 ;16.299 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;15.576 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1150 ; 0.192 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8536 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1538 ; 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): 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6Z2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976280 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 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93417 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 79.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1JV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M TRIS, PH 8.5, 30% REMARK 280 PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K 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: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 LEU A 0 REMARK 465 MET A 1 REMARK 465 GLY A 55 REMARK 465 PHE A 56 REMARK 465 ASN A 57 REMARK 465 GLN A 58 REMARK 465 SER A 59 REMARK 465 SER A 60 REMARK 465 TYR A 61 REMARK 465 GLN A 62 REMARK 465 LYS A 63 REMARK 465 ASN A 64 REMARK 465 VAL A 65 REMARK 465 ASP A 66 REMARK 465 ALA A 67 REMARK 465 ARG A 68 REMARK 465 GLU A 75 REMARK 465 VAL A 76 REMARK 465 LEU A 77 REMARK 465 GLY A 78 REMARK 465 SER A 79 REMARK 465 ALA A 80 REMARK 465 THR A 81 REMARK 465 ARG A 82 REMARK 465 ASP A 83 REMARK 465 GLN A 84 REMARK 465 GLY A 110 REMARK 465 GLY A 111 REMARK 465 GLN A 112 REMARK 465 GLY A 113 REMARK 465 THR A 114 REMARK 465 ARG A 169 REMARK 465 ASP A 296 REMARK 465 LYS A 502 REMARK 465 ASN A 503 REMARK 465 GLY A 504 REMARK 465 ILE A 505 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLU B -1 REMARK 465 LEU B 0 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ASN B 57 REMARK 465 GLN B 58 REMARK 465 SER B 59 REMARK 465 SER B 60 REMARK 465 TYR B 61 REMARK 465 GLN B 62 REMARK 465 LYS B 63 REMARK 465 ASN B 64 REMARK 465 ARG B 74 REMARK 465 GLU B 75 REMARK 465 VAL B 76 REMARK 465 LEU B 77 REMARK 465 GLY B 78 REMARK 465 SER B 79 REMARK 465 ALA B 80 REMARK 465 THR B 81 REMARK 465 ARG B 82 REMARK 465 ASP B 83 REMARK 465 GLN B 84 REMARK 465 ASP B 85 REMARK 465 GLN B 86 REMARK 465 ASP B 362 REMARK 465 THR B 363 REMARK 465 VAL B 501 REMARK 465 LYS B 502 REMARK 465 ASN B 503 REMARK 465 GLY B 504 REMARK 465 ILE B 505 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 ARG A 74 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 YCM B 251 C VAL B 252 N 0.264 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 VAL A 344 -52.27 -128.00 REMARK 500 ASN A 413 12.44 -146.15 REMARK 500 ALA A 473 33.75 -146.89 REMARK 500 ASP B 221 31.84 -96.54 REMARK 500 SER B 411 -8.44 71.38 REMARK 500 ASN B 413 16.07 -147.45 REMARK 500 ALA B 473 27.83 -143.34 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 B1062 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B1063 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B1064 DISTANCE = 6.64 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UD1 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UD1 B 601 DBREF 6Z2F A 1 505 UNP Q16222 UAP1_HUMAN 1 505 DBREF 6Z2F B 1 505 UNP Q16222 UAP1_HUMAN 1 505 SEQADV 6Z2F GLY A -3 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F PRO A -2 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F GLU A -1 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F LEU A 0 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F TYR A 61 UNP Q16222 HIS 61 CONFLICT SEQADV 6Z2F THR A 229 UNP Q16222 ALA 229 ENGINEERED MUTATION SEQADV 6Z2F GLY B -3 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F PRO B -2 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F GLU B -1 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F LEU B 0 UNP Q16222 EXPRESSION TAG SEQADV 6Z2F TYR B 61 UNP Q16222 HIS 61 CONFLICT SEQADV 6Z2F THR B 229 UNP Q16222 ALA 229 ENGINEERED MUTATION SEQRES 1 A 509 GLY PRO GLU LEU MET ASN ILE ASN ASP LEU LYS LEU THR SEQRES 2 A 509 LEU SER LYS ALA GLY GLN GLU HIS LEU LEU ARG PHE TRP SEQRES 3 A 509 ASN GLU LEU GLU GLU ALA GLN GLN VAL GLU LEU TYR ALA SEQRES 4 A 509 GLU LEU GLN ALA MET ASN PHE GLU GLU LEU ASN PHE PHE SEQRES 5 A 509 PHE GLN LYS ALA ILE GLU GLY PHE ASN GLN SER SER TYR SEQRES 6 A 509 GLN LYS ASN VAL ASP ALA ARG MET GLU PRO VAL PRO ARG SEQRES 7 A 509 GLU VAL LEU GLY SER ALA THR ARG ASP GLN ASP GLN LEU SEQRES 8 A 509 GLN ALA TRP GLU SER GLU GLY LEU PHE GLN ILE SER GLN SEQRES 9 A 509 ASN LYS VAL ALA VAL LEU LEU LEU ALA GLY GLY GLN GLY SEQRES 10 A 509 THR ARG LEU GLY VAL ALA TYR PRO LYS GLY MET TYR ASP SEQRES 11 A 509 VAL GLY LEU PRO SER ARG LYS THR LEU PHE GLN ILE GLN SEQRES 12 A 509 ALA GLU ARG ILE LEU LYS LEU GLN GLN VAL ALA GLU LYS SEQRES 13 A 509 TYR TYR GLY ASN LYS CYS ILE ILE PRO TRP TYR ILE MET SEQRES 14 A 509 THR SER GLY ARG THR MET GLU SER THR LYS GLU PHE PHE SEQRES 15 A 509 THR LYS HIS LYS TYR PHE GLY LEU LYS LYS GLU ASN VAL SEQRES 16 A 509 ILE PHE PHE GLN GLN GLY MET LEU PRO ALA MET SER PHE SEQRES 17 A 509 ASP GLY LYS ILE ILE LEU GLU GLU LYS ASN LYS VAL SER SEQRES 18 A 509 MET ALA PRO ASP GLY ASN GLY GLY LEU TYR ARG THR LEU SEQRES 19 A 509 ALA ALA GLN ASN ILE VAL GLU ASP MET GLU GLN ARG GLY SEQRES 20 A 509 ILE TRP SER ILE HIS VAL TYR CYS VAL ASP ASN ILE LEU SEQRES 21 A 509 VAL LYS VAL ALA ASP PRO ARG PHE ILE GLY PHE CYS ILE SEQRES 22 A 509 GLN LYS GLY ALA ASP CYS GLY ALA LYS VAL VAL GLU LYS SEQRES 23 A 509 THR ASN PRO THR GLU PRO VAL GLY VAL VAL CYS ARG VAL SEQRES 24 A 509 ASP GLY VAL TYR GLN VAL VAL GLU TYR SER GLU ILE SER SEQRES 25 A 509 LEU ALA THR ALA GLN LYS ARG SER SER ASP GLY ARG LEU SEQRES 26 A 509 LEU PHE ASN ALA GLY ASN ILE ALA ASN HIS PHE PHE THR SEQRES 27 A 509 VAL PRO PHE LEU ARG ASP VAL VAL ASN VAL TYR GLU PRO SEQRES 28 A 509 GLN LEU GLN HIS HIS VAL ALA GLN LYS LYS ILE PRO TYR SEQRES 29 A 509 VAL ASP THR GLN GLY GLN LEU ILE LYS PRO ASP LYS PRO SEQRES 30 A 509 ASN GLY ILE LYS MET GLU LYS PHE VAL PHE ASP ILE PHE SEQRES 31 A 509 GLN PHE ALA LYS LYS PHE VAL VAL TYR GLU VAL LEU ARG SEQRES 32 A 509 GLU ASP GLU PHE SER PRO LEU LYS ASN ALA ASP SER GLN SEQRES 33 A 509 ASN GLY LYS ASP ASN PRO THR THR ALA ARG HIS ALA LEU SEQRES 34 A 509 MET SER LEU HIS HIS CYS TRP VAL LEU ASN ALA GLY GLY SEQRES 35 A 509 HIS PHE ILE ASP GLU ASN GLY SER ARG LEU PRO ALA ILE SEQRES 36 A 509 PRO ARG LEU LYS ASP ALA ASN ASP VAL PRO ILE GLN CYS SEQRES 37 A 509 GLU ILE SER PRO LEU ILE SER TYR ALA GLY GLU GLY LEU SEQRES 38 A 509 GLU SER TYR VAL ALA ASP LYS GLU PHE HIS ALA PRO LEU SEQRES 39 A 509 ILE ILE ASP GLU ASN GLY VAL HIS GLU LEU VAL LYS ASN SEQRES 40 A 509 GLY ILE SEQRES 1 B 509 GLY PRO GLU LEU MET ASN ILE ASN ASP LEU LYS LEU THR SEQRES 2 B 509 LEU SER LYS ALA GLY GLN GLU HIS LEU LEU ARG PHE TRP SEQRES 3 B 509 ASN GLU LEU GLU GLU ALA GLN GLN VAL GLU LEU TYR ALA SEQRES 4 B 509 GLU LEU GLN ALA MET ASN PHE GLU GLU LEU ASN PHE PHE SEQRES 5 B 509 PHE GLN LYS ALA ILE GLU GLY PHE ASN GLN SER SER TYR SEQRES 6 B 509 GLN LYS ASN VAL ASP ALA ARG MET GLU PRO VAL PRO ARG SEQRES 7 B 509 GLU VAL LEU GLY SER ALA THR ARG ASP GLN ASP GLN LEU SEQRES 8 B 509 GLN ALA TRP GLU SER GLU GLY LEU PHE GLN ILE SER GLN SEQRES 9 B 509 ASN LYS VAL ALA VAL LEU LEU LEU ALA GLY GLY GLN GLY SEQRES 10 B 509 THR ARG LEU GLY VAL ALA TYR PRO LYS GLY MET TYR ASP SEQRES 11 B 509 VAL GLY LEU PRO SER ARG LYS THR LEU PHE GLN ILE GLN SEQRES 12 B 509 ALA GLU ARG ILE LEU LYS LEU GLN GLN VAL ALA GLU LYS SEQRES 13 B 509 TYR TYR GLY ASN LYS CYS ILE ILE PRO TRP TYR ILE MET SEQRES 14 B 509 THR SER GLY ARG THR MET GLU SER THR LYS GLU PHE PHE SEQRES 15 B 509 THR LYS HIS LYS TYR PHE GLY LEU LYS LYS GLU ASN VAL SEQRES 16 B 509 ILE PHE PHE GLN GLN GLY MET LEU PRO ALA MET SER PHE SEQRES 17 B 509 ASP GLY LYS ILE ILE LEU GLU GLU LYS ASN LYS VAL SER SEQRES 18 B 509 MET ALA PRO ASP GLY ASN GLY GLY LEU TYR ARG THR LEU SEQRES 19 B 509 ALA ALA GLN ASN ILE VAL GLU ASP MET GLU GLN ARG GLY SEQRES 20 B 509 ILE TRP SER ILE HIS VAL TYR YCM VAL ASP ASN ILE LEU SEQRES 21 B 509 VAL LYS VAL ALA ASP PRO ARG PHE ILE GLY PHE CYS ILE SEQRES 22 B 509 GLN LYS GLY ALA ASP CYS GLY ALA LYS VAL VAL GLU LYS SEQRES 23 B 509 THR ASN PRO THR GLU PRO VAL GLY VAL VAL CYS ARG VAL SEQRES 24 B 509 ASP GLY VAL TYR GLN VAL VAL GLU TYR SER GLU ILE SER SEQRES 25 B 509 LEU ALA THR ALA GLN LYS ARG SER SER ASP GLY ARG LEU SEQRES 26 B 509 LEU PHE ASN ALA GLY ASN ILE ALA ASN HIS PHE PHE THR SEQRES 27 B 509 VAL PRO PHE LEU ARG ASP VAL VAL ASN VAL TYR GLU PRO SEQRES 28 B 509 GLN LEU GLN HIS HIS VAL ALA GLN LYS LYS ILE PRO TYR SEQRES 29 B 509 VAL ASP THR GLN GLY GLN LEU ILE LYS PRO ASP LYS PRO SEQRES 30 B 509 ASN GLY ILE LYS MET GLU LYS PHE VAL PHE ASP ILE PHE SEQRES 31 B 509 GLN PHE ALA LYS LYS PHE VAL VAL TYR GLU VAL LEU ARG SEQRES 32 B 509 GLU ASP GLU PHE SER PRO LEU LYS ASN ALA ASP SER GLN SEQRES 33 B 509 ASN GLY LYS ASP ASN PRO THR THR ALA ARG HIS ALA LEU SEQRES 34 B 509 MET SER LEU HIS HIS CYS TRP VAL LEU ASN ALA GLY GLY SEQRES 35 B 509 HIS PHE ILE ASP GLU ASN GLY SER ARG LEU PRO ALA ILE SEQRES 36 B 509 PRO ARG LEU LYS ASP ALA ASN ASP VAL PRO ILE GLN CYS SEQRES 37 B 509 GLU ILE SER PRO LEU ILE SER TYR ALA GLY GLU GLY LEU SEQRES 38 B 509 GLU SER TYR VAL ALA ASP LYS GLU PHE HIS ALA PRO LEU SEQRES 39 B 509 ILE ILE ASP GLU ASN GLY VAL HIS GLU LEU VAL LYS ASN SEQRES 40 B 509 GLY ILE MODRES 6Z2F YCM B 251 CYS MODIFIED RESIDUE HET YCM B 251 10 HET UD1 A 601 39 HET UD1 B 601 39 HETNAM YCM S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE HETNAM UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE HETSYN YCM CYSTEINE-S-ACETAMIDE FORMUL 2 YCM C5 H10 N2 O3 S FORMUL 3 UD1 2(C17 H27 N3 O17 P2) FORMUL 5 HOH *701(H2 O) HELIX 1 AA1 ASN A 2 ALA A 13 1 12 HELIX 2 AA2 GLN A 15 ARG A 20 5 6 HELIX 3 AA3 PHE A 21 LEU A 25 5 5 HELIX 4 AA4 GLU A 26 ALA A 39 1 14 HELIX 5 AA5 ASN A 41 ILE A 53 1 13 HELIX 6 AA6 GLN A 86 GLN A 100 1 15 HELIX 7 AA7 PRO A 121 TYR A 125 5 5 HELIX 8 AA8 THR A 134 GLY A 155 1 22 HELIX 9 AA9 MET A 171 HIS A 181 1 11 HELIX 10 AB1 LYS A 182 LEU A 186 5 5 HELIX 11 AB2 LYS A 187 GLU A 189 5 3 HELIX 12 AB3 GLY A 222 GLY A 224 5 3 HELIX 13 AB4 GLY A 225 GLN A 233 1 9 HELIX 14 AB5 ASN A 234 GLY A 243 1 10 HELIX 15 AB6 ASP A 261 GLY A 272 1 12 HELIX 16 AB7 GLU A 303 ILE A 307 5 5 HELIX 17 AB8 SER A 308 LYS A 314 1 7 HELIX 18 AB9 VAL A 335 VAL A 344 1 10 HELIX 19 AC1 TYR A 345 LEU A 349 5 5 HELIX 20 AC2 PHE A 381 ALA A 389 5 9 HELIX 21 AC3 LEU A 398 PHE A 403 1 6 HELIX 22 AC4 ASN A 417 ALA A 436 1 20 HELIX 23 AC5 LEU A 477 ALA A 482 1 6 HELIX 24 AC6 ASN B 4 GLY B 14 1 11 HELIX 25 AC7 GLN B 15 ARG B 20 5 6 HELIX 26 AC8 PHE B 21 LEU B 25 5 5 HELIX 27 AC9 GLU B 26 ALA B 39 1 14 HELIX 28 AD1 ASN B 41 PHE B 56 1 16 HELIX 29 AD2 VAL B 65 ALA B 67 5 3 HELIX 30 AD3 GLN B 88 GLN B 100 1 13 HELIX 31 AD4 GLY B 113 GLY B 117 5 5 HELIX 32 AD5 PRO B 121 TYR B 125 5 5 HELIX 33 AD6 THR B 134 GLY B 155 1 22 HELIX 34 AD7 THR B 170 HIS B 181 1 12 HELIX 35 AD8 LYS B 182 LEU B 186 5 5 HELIX 36 AD9 LYS B 187 GLU B 189 5 3 HELIX 37 AE1 GLY B 222 GLY B 224 5 3 HELIX 38 AE2 GLY B 225 GLN B 233 1 9 HELIX 39 AE3 ASN B 234 GLY B 243 1 10 HELIX 40 AE4 ASP B 261 LYS B 271 1 11 HELIX 41 AE5 SER B 308 LYS B 314 1 7 HELIX 42 AE6 VAL B 335 VAL B 344 1 10 HELIX 43 AE7 TYR B 345 LEU B 349 5 5 HELIX 44 AE8 PHE B 381 ALA B 389 5 9 HELIX 45 AE9 LEU B 398 PHE B 403 1 6 HELIX 46 AF1 ASN B 417 ALA B 436 1 20 HELIX 47 AF2 LEU B 477 ALA B 482 1 6 SHEET 1 AA1 7 VAL A 191 GLN A 195 0 SHEET 2 AA1 7 TRP A 162 THR A 166 1 N ILE A 164 O ILE A 192 SHEET 3 AA1 7 VAL A 103 LEU A 108 1 N VAL A 105 O TYR A 163 SHEET 4 AA1 7 SER A 246 CYS A 251 1 O TYR A 250 N LEU A 108 SHEET 5 AA1 7 ALA A 325 THR A 334 -1 O PHE A 333 N ILE A 247 SHEET 6 AA1 7 CYS A 275 GLU A 281 -1 N LYS A 278 O ASN A 330 SHEET 7 AA1 7 PHE A 392 GLU A 396 1 O TYR A 395 N ALA A 277 SHEET 1 AA2 2 MET A 198 PRO A 200 0 SHEET 2 AA2 2 MET A 218 PRO A 220 -1 O ALA A 219 N LEU A 199 SHEET 1 AA3 2 LEU A 210 GLU A 212 0 SHEET 2 AA3 2 LYS A 215 VAL A 216 -1 O LYS A 215 N GLU A 211 SHEET 1 AA4 2 VAL A 291 ARG A 294 0 SHEET 2 AA4 2 TYR A 299 VAL A 302 -1 O VAL A 302 N VAL A 291 SHEET 1 AA5 2 HIS A 352 LYS A 356 0 SHEET 2 AA5 2 GLY A 375 GLU A 379 -1 O GLU A 379 N HIS A 352 SHEET 1 AA6 2 TYR A 360 VAL A 361 0 SHEET 2 AA6 2 LEU A 367 ILE A 368 -1 O ILE A 368 N TYR A 360 SHEET 1 AA7 2 HIS A 439 PHE A 440 0 SHEET 2 AA7 2 GLU A 485 PHE A 486 1 O PHE A 486 N HIS A 439 SHEET 1 AA8 3 CYS A 464 ILE A 466 0 SHEET 2 AA8 3 LEU A 490 ASP A 493 1 O ILE A 492 N GLU A 465 SHEET 3 AA8 3 GLY A 496 GLU A 499 -1 O HIS A 498 N ILE A 491 SHEET 1 AA9 3 MET B 69 GLU B 70 0 SHEET 2 AA9 3 VAL B 291 VAL B 295 -1 O ARG B 294 N GLU B 70 SHEET 3 AA9 3 VAL B 298 VAL B 302 -1 O VAL B 298 N VAL B 295 SHEET 1 AB1 7 VAL B 191 GLN B 195 0 SHEET 2 AB1 7 TRP B 162 THR B 166 1 N ILE B 164 O ILE B 192 SHEET 3 AB1 7 VAL B 103 GLY B 110 1 N LEU B 107 O TYR B 163 SHEET 4 AB1 7 SER B 246 YCM B 251 1 O HIS B 248 N LEU B 106 SHEET 5 AB1 7 ALA B 325 THR B 334 -1 O HIS B 331 N VAL B 249 SHEET 6 AB1 7 CYS B 275 GLU B 281 -1 N LYS B 278 O ASN B 330 SHEET 7 AB1 7 PHE B 392 VAL B 397 1 O VAL B 397 N VAL B 279 SHEET 1 AB2 2 MET B 198 PRO B 200 0 SHEET 2 AB2 2 MET B 218 PRO B 220 -1 O ALA B 219 N LEU B 199 SHEET 1 AB3 3 MET B 202 SER B 203 0 SHEET 2 AB3 3 GLY B 375 GLU B 379 -1 O ILE B 376 N MET B 202 SHEET 3 AB3 3 HIS B 352 LYS B 356 -1 N HIS B 352 O GLU B 379 SHEET 1 AB4 2 LEU B 210 GLU B 212 0 SHEET 2 AB4 2 LYS B 215 VAL B 216 -1 O LYS B 215 N GLU B 211 SHEET 1 AB5 2 HIS B 439 PHE B 440 0 SHEET 2 AB5 2 GLU B 485 PHE B 486 1 O PHE B 486 N HIS B 439 SHEET 1 AB6 3 CYS B 464 ILE B 466 0 SHEET 2 AB6 3 LEU B 490 ASP B 493 1 O LEU B 490 N GLU B 465 SHEET 3 AB6 3 GLY B 496 GLU B 499 -1 O HIS B 498 N ILE B 491 LINK C TYR B 250 N YCM B 251 1555 1555 1.33 LINK C YCM B 251 N VAL B 252 1555 1555 1.60 CISPEP 1 ALA A 488 PRO A 489 0 3.21 CISPEP 2 ALA B 488 PRO B 489 0 3.45 SITE 1 AC1 21 LEU A 108 MET A 165 GLN A 196 PRO A 220 SITE 2 AC1 21 GLY A 222 ASN A 223 CYS A 251 VAL A 252 SITE 3 AC1 21 VAL A 289 GLY A 290 GLU A 303 TYR A 304 SITE 4 AC1 21 ASN A 327 PHE A 381 PHE A 383 PHE A 403 SITE 5 AC1 21 LYS A 407 HOH A 860 HOH A 887 HOH A 919 SITE 6 AC1 21 LYS B 455 SITE 1 AC2 26 ARG A 453 GLY B 110 GLY B 111 GLN B 112 SITE 2 AC2 26 GLY B 113 THR B 114 ARG B 115 LYS B 122 SITE 3 AC2 26 ASN B 223 YCM B 251 VAL B 289 GLY B 290 SITE 4 AC2 26 GLU B 303 TYR B 304 ASN B 327 PHE B 381 SITE 5 AC2 26 PHE B 383 LYS B 407 HOH B 712 HOH B 719 SITE 6 AC2 26 HOH B 745 HOH B 750 HOH B 751 HOH B 753 SITE 7 AC2 26 HOH B 768 HOH B 953 CRYST1 45.614 64.569 82.070 95.63 101.09 104.93 P 1 1 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 0.021923 0.005846 0.005272 0.00000 SCALE2 0.000000 0.016029 0.002526 0.00000 SCALE3 0.000000 0.000000 0.012570 0.00000