HEADER LYASE 28-APR-20 6YVL TITLE HUMAN OMPD-DOMAIN OF UMPS IN COMPLEX WITH THE SUBSTRATE OMP AT 1.25 TITLE 2 ANGSTROMS RESOLUTION, 1.42 MGY EXPOSURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UMP SYNTHASE; COMPND 5 EC: 2.4.2.10,4.1.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CYSTEINE MODIFICATION ON POSITION 304 UAG STOP-CODON COMPND 8 MEDIATED INTRODUCTION OF ACETYLATED LYSINE RESIDUE (ACK314) EXPOSURE COMPND 9 1.42 MGY SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UMPS, OK/SW-CL.21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OMPD, OMP, UMPS, OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TITTMANN,S.RINDFLEISCH,M.KRULL REVDAT 4 13-NOV-24 6YVL 1 REMARK REVDAT 3 24-JAN-24 6YVL 1 REMARK REVDAT 2 04-MAY-22 6YVL 1 JRNL REVDAT 1 17-NOV-21 6YVL 0 JRNL AUTH S.RINDFLEISCH,M.KRULL,J.URANGA,T.SCHMIDT, JRNL AUTH 2 F.RABE VON PAPPENHEIM,L.L.KIRCK,A.BALOURI,T.SCHNEIDER, JRNL AUTH 3 A.CHARI,R.KLUGER,G.BOURENKOV,U.DIEDERICHSEN,R.A.MATA, JRNL AUTH 4 K.TITTMANN JRNL TITL GROUND-STATE DESTABILIZATION BY ELECTROSTATIC REPULSION IS JRNL TITL 2 NOT A DRIVING FORCE IN OROTIDINE-5-MONOPHOSPHATE JRNL TITL 3 DECARBOXYLASE CATALYSIS JRNL REF NAT CATAL V. 5 332 2022 JRNL REFN ESSN 2520-1158 JRNL DOI 10.1038/S41929-022-00771-W REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 73773 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) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3767 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5390 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 269 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1962 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : -0.40000 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): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.039 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 : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2545 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2370 ; 0.035 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3495 ; 1.461 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5539 ; 2.263 ; 1.596 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 6.699 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;32.147 ;22.541 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;12.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.691 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 325 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2951 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 518 ; 0.014 ; 0.021 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): 4914 ; 9.253 ; 3.000 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6YVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107247. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.82660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77540 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 19.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.818 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.84 REMARK 200 R MERGE FOR SHELL (I) : 1.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.690 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: 2QCD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION: 100 MM TRIS/HCL PH REMARK 280 8.0, 1.9 - 2.1 M AMMONIUM SULFATE, 10 MM GLUTATHION, 5% (V/V) REMARK 280 GLYCEROL SOAKING: 100 MM TRIS/HCL PH 8.0, 2.0 M AMMONIUM SULFATE, REMARK 280 10 MM GLUTATHION, 5% (V/V) GLYCEROL, 50 MM OMP CRYO-PROTECTION: REMARK 280 100 MM TRIS/HCL PH 8.0, 2.0 M AMMONIUM SULFATE, 10 MM GLUTATHION, REMARK 280 5% (V/V) GLYCEROL, 50 MM OMP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 30.98500 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 30.98500 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 38.65500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.42500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.65500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.42500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.98500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.65500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.42500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.98500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.65500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.42500 REMARK 290 SMTRY3 8 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: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.97000 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 A 778 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 221 REMARK 465 ALA A 222 REMARK 465 MET A 223 REMARK 465 VAL A 480 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 285 5.91 -66.75 REMARK 500 GLU A 306 75.55 68.98 REMARK 500 ALA A 316 35.30 -160.37 REMARK 500 GLU A 391 3.92 -58.18 REMARK 500 PHE A 396 -39.41 -131.31 REMARK 500 PHE A 396 -39.41 -130.42 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 A 926 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 927 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 928 DISTANCE = 6.45 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OMP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 509 DBREF 6YVL A 224 480 UNP P11172 UMPS_HUMAN 46 302 SEQADV 6YVL GLY A 221 UNP P11172 EXPRESSION TAG SEQADV 6YVL ALA A 222 UNP P11172 EXPRESSION TAG SEQADV 6YVL MET A 223 UNP P11172 EXPRESSION TAG SEQRES 1 A 260 GLY ALA MET GLU LEU SER PHE GLY ALA ARG ALA GLU LEU SEQRES 2 A 260 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU SEQRES 3 A 260 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP SEQRES 4 A 260 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA SEQRES 5 A 260 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP SEQRES 6 A 260 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU SEQRES 7 A 260 ILE THR LEU ALA LYS CSS HIS GLU PHE LEU ILE PHE GLU SEQRES 8 A 260 ASP ARG ALY PHE ALA ASP ILE GLY ASN THR VAL LYS LYS SEQRES 9 A 260 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA SEQRES 10 A 260 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL SEQRES 11 A 260 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG SEQRES 12 A 260 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER SEQRES 13 A 260 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET SEQRES 14 A 260 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER SEQRES 15 A 260 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU SEQRES 16 A 260 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU SEQRES 17 A 260 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS SEQRES 18 A 260 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE SEQRES 19 A 260 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG SEQRES 20 A 260 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL MODRES 6YVL CSS A 304 CYS MODIFIED RESIDUE MODRES 6YVL ALY A 314 LYS MODIFIED RESIDUE HET CSS A 304 7 HET ALY A 314 12 HET OMP A 501 24 HET U A 502 21 HET GOL A 503 6 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET SO4 A 509 5 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM ALY N(6)-ACETYLLYSINE HETNAM OMP OROTIDINE-5'-MONOPHOSPHATE HETNAM U URIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 1 ALY C8 H16 N2 O3 FORMUL 2 OMP C10 H13 N2 O11 P FORMUL 3 U C9 H13 N2 O9 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 SO4 6(O4 S 2-) FORMUL 11 HOH *328(H2 O) HELIX 1 AA1 SER A 226 ALA A 231 1 6 HELIX 2 AA2 HIS A 237 GLU A 251 1 15 HELIX 3 AA3 LEU A 262 GLY A 274 1 13 HELIX 4 AA4 PRO A 275 ILE A 277 5 3 HELIX 5 AA5 HIS A 283 LEU A 287 5 5 HELIX 6 AA6 THR A 291 GLU A 306 1 16 HELIX 7 AA7 ILE A 318 GLY A 328 1 11 HELIX 8 AA8 LYS A 332 ALA A 337 1 6 HELIX 9 AA9 SER A 348 LEU A 359 1 12 HELIX 10 AB1 GLY A 380 GLU A 392 1 13 HELIX 11 AB2 SER A 434 LYS A 441 1 8 HELIX 12 AB3 GLY A 450 SER A 455 1 6 HELIX 13 AB4 ASP A 458 GLY A 479 1 22 SHEET 1 AA1 9 LEU A 254 SER A 257 0 SHEET 2 AA1 9 MET A 279 THR A 282 1 O LYS A 281 N LEU A 256 SHEET 3 AA1 9 LEU A 308 PHE A 315 1 O ASP A 312 N THR A 282 SHEET 4 AA1 9 LEU A 339 HIS A 343 1 O HIS A 343 N PHE A 315 SHEET 5 AA1 9 GLY A 364 ILE A 368 1 O ILE A 368 N ALA A 342 SHEET 6 AA1 9 VAL A 397 ILE A 401 1 O VAL A 398 N CYS A 365 SHEET 7 AA1 9 LEU A 413 THR A 416 1 O LEU A 415 N PHE A 400 SHEET 8 AA1 9 ILE A 446 VAL A 449 1 O ILE A 446 N THR A 416 SHEET 9 AA1 9 LEU A 254 SER A 257 1 N CYS A 255 O ILE A 447 LINK C ALYS A 303 N CSS A 304 1555 1555 1.34 LINK C BLYS A 303 N CSS A 304 1555 1555 1.34 LINK C CSS A 304 N HIS A 305 1555 1555 1.33 LINK C ARG A 313 N ALY A 314 1555 1555 1.34 LINK C ALY A 314 N PHE A 315 1555 1555 1.34 SITE 1 AC1 22 SER A 257 ASP A 259 LYS A 281 HIS A 283 SITE 2 AC1 22 ASP A 312 ALY A 314 ASP A 317 ILE A 318 SITE 3 AC1 22 THR A 321 ASN A 341 MET A 371 SER A 372 SITE 4 AC1 22 PRO A 417 GLN A 430 TYR A 432 GLY A 450 SITE 5 AC1 22 ARG A 451 U A 502 HOH A 630 HOH A 638 SITE 6 AC1 22 HOH A 675 HOH A 767 SITE 1 AC2 20 SER A 257 ASP A 259 LYS A 281 HIS A 283 SITE 2 AC2 20 ASP A 312 ALY A 314 ASP A 317 ILE A 318 SITE 3 AC2 20 THR A 321 MET A 371 SER A 372 PRO A 417 SITE 4 AC2 20 GLN A 430 TYR A 432 GLY A 450 ARG A 451 SITE 5 AC2 20 OMP A 501 HOH A 630 HOH A 638 HOH A 675 SITE 1 AC3 5 ARG A 235 LYS A 468 HOH A 609 HOH A 912 SITE 2 AC3 5 HOH A 920 SITE 1 AC4 5 THR A 374 GLY A 429 HOH A 619 HOH A 624 SITE 2 AC4 5 HOH A 639 SITE 1 AC5 1 ARG A 235 SITE 1 AC6 3 ASN A 433 ARG A 442 HOH A 604 SITE 1 AC7 2 GLY A 380 ARG A 384 SITE 1 AC8 4 SER A 348 LYS A 352 HIS A 393 HOH A 634 SITE 1 AC9 4 ARG A 388 HOH A 643 HOH A 660 HOH A 733 CRYST1 77.310 116.850 61.970 90.00 90.00 90.00 C 2 2 21 8 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 0.012935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016137 0.00000