10 20 30 40 50 60 70 80 3EX4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 16-OCT-08 3EX4
TITLE HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX TITLE 2 WITH BMP
COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE-5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 224-480; COMPND 5 SYNONYM: OMPDECASE; COMPND 6 EC: 4.1.1.23; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: UMPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-30
KEYWDS DECARBOXYLASE, TIM BARREL, UNUSUAL CATALYSIS, ALTERNATIVE KEYWDS 2 SPLICING, DISEASE MUTATION, GLYCOSYLTRANSFERASE, LYASE, KEYWDS 3 MULTIFUNCTIONAL ENZYME, POLYMORPHISM, PYRIMIDINE KEYWDS 4 BIOSYNTHESIS, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.HEINRICH,U.DIEDERICHSEN,M.RUDOLPH
REVDAT 2 15-DEC-09 3EX4 1 JRNL REVDAT 1 07-APR-09 3EX4 0
JRNL AUTH D.HEINRICH,U.DIEDERICHSEN,M.G.RUDOLPH JRNL TITL LYS314 IS A NUCLEOPHILE IN NON-CLASSICAL REACTIONS JRNL TITL 2 OF OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE JRNL REF CHEMISTRY V. 15 6619 2009 JRNL REFN ISSN 0947-6539 JRNL PMID 19472232 JRNL DOI 10.1002/CHEM.200900397
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0077 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 73733 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) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.135 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3928 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) : 1.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 245 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2096 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : -0.01000 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): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.984 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 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): 2176 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1489 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2974 ; 1.607 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3670 ; 3.184 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 5.947 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;31.723 ;23.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 407 ;12.932 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;14.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 346 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2439 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 433 ; 0.003 ; 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): 1346 ; 1.438 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 554 ; 0.714 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2182 ; 2.187 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 830 ; 3.230 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 770 ; 4.939 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3665 ; 1.523 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 345 ; 7.292 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3607 ; 3.017 ; 3.000 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 : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3EX4 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-08. REMARK 100 THE RCSB ID CODE IS RCSB049876.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 44.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COMO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.0, 1.8 M (NH4) REMARK 280 2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 300.0K
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 31.03000 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 31.03000 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 38.66000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.66000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.03000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.66000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.45000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.03000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.66000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.45000 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: 3700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.4 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 62.06000
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 816 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 495 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 VAL A 480
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 682 O HOH A 782 2.00 REMARK 500 O HOH A 801 O HOH A 824 2.02 REMARK 500 O HOH A 634 O HOH A 824 2.12 REMARK 500 O HOH A 714 O HOH A 731 2.13 REMARK 500 O HOH A 656 O HOH A 711 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 477 NE - CZ - NH2 ANGL. DEV. = 3.1 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 306 76.35 66.10 REMARK 500 ALA A 316 34.50 -160.85 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 662 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 5.71 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMP A 481
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EWU RELATED DB: PDB REMARK 900 D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE IN COMPLEX WITH 6-ACETYL-UMP, COVALENT ADDUCT REMARK 900 RELATED ID: 3EWW RELATED DB: PDB REMARK 900 D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE IN COMPLEX WITH 6-CYANO-UMP, COVALENT ADDUCT REMARK 900 RELATED ID: 3EWX RELATED DB: PDB REMARK 900 K314A MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE IN COMPLEX WITH 6-AZIDO-UMP, DEGRADED TO BMP REMARK 900 RELATED ID: 3EWY RELATED DB: PDB REMARK 900 K314A MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE SOAKED WITH OMP, DECARBOXYLATED TO UMP REMARK 900 RELATED ID: 3EWZ RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX REMARK 900 WITH 5-CYANO-UMP REMARK 900 RELATED ID: 3EX0 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX REMARK 900 WITH 6-ACETYL-UMP REMARK 900 RELATED ID: 3EX1 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE SOAKED WITH REMARK 900 6-CYANO-UMP, CONVERTED TO UMP REMARK 900 RELATED ID: 3EX2 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX REMARK 900 WITH 6-CYANO-UMP REMARK 900 RELATED ID: 3EX3 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX REMARK 900 WITH 6-AZIDO-UMP, COVALENT ADDUCT REMARK 900 RELATED ID: 3EX5 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX REMARK 900 WITH 6-MERCAPTO-UMP REMARK 900 RELATED ID: 3EX6 RELATED DB: PDB REMARK 900 D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE IN COMPLEX WITH 6-AZIDO-UMP, COVALENT ADDUCT
DBREF 3EX4 A 224 480 UNP P11172 PYR5_HUMAN 224 480
SEQADV 3EX4 GLY A 221 UNP P11172 EXPRESSION TAG SEQADV 3EX4 ALA A 222 UNP P11172 EXPRESSION TAG SEQADV 3EX4 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 CYS HIS GLU PHE LEU ILE PHE GLU SEQRES 8 A 260 ASP ARG LYS 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
HET BMP A 481 22
HETNAM BMP 6-HYDROXYURIDINE-5'-PHOSPHATE
FORMUL 2 BMP C9 H13 N2 O10 P FORMUL 3 HOH *345(H2 O)
HELIX 1 1 SER A 226 ALA A 231 1 6 HELIX 2 2 HIS A 237 GLU A 251 1 15 HELIX 3 3 LEU A 262 GLY A 274 1 13 HELIX 4 4 PRO A 275 ILE A 277 5 3 HELIX 5 5 HIS A 283 LEU A 287 5 5 HELIX 6 6 THR A 291 GLU A 306 1 16 HELIX 7 7 ILE A 318 GLY A 328 1 11 HELIX 8 8 LYS A 332 ALA A 337 1 6 HELIX 9 9 SER A 348 LEU A 359 1 12 HELIX 10 10 THR A 379 HIS A 393 1 15 HELIX 11 11 SER A 434 LYS A 441 1 8 HELIX 12 12 GLY A 450 SER A 455 1 6 HELIX 13 13 ASP A 458 GLY A 479 1 22
SHEET 1 A 9 LEU A 254 SER A 257 0 SHEET 2 A 9 MET A 279 THR A 282 1 O LYS A 281 N LEU A 256 SHEET 3 A 9 LEU A 308 PHE A 315 1 O ASP A 312 N THR A 282 SHEET 4 A 9 LEU A 339 HIS A 343 1 O HIS A 343 N PHE A 315 SHEET 5 A 9 GLY A 364 ILE A 368 1 O ILE A 368 N ALA A 342 SHEET 6 A 9 VAL A 397 ILE A 401 1 O VAL A 398 N CYS A 365 SHEET 7 A 9 LEU A 413 THR A 416 1 O LEU A 413 N PHE A 400 SHEET 8 A 9 ILE A 446 VAL A 449 1 O ILE A 446 N THR A 416 SHEET 9 A 9 LEU A 254 SER A 257 1 N CYS A 255 O ILE A 447
SITE 1 AC1 21 SER A 257 ASP A 259 LYS A 281 HIS A 283 SITE 2 AC1 21 ASP A 312 LYS A 314 ASP A 317 ILE A 318 SITE 3 AC1 21 THR A 321 MET A 371 SER A 372 PRO A 417 SITE 4 AC1 21 GLN A 430 TYR A 432 GLY A 450 ARG A 451 SITE 5 AC1 21 HOH A 483 HOH A 484 HOH A 494 HOH A 498 SITE 6 AC1 21 HOH A 517
CRYST1 77.320 116.900 62.060 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 0.012933 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008554 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016113 0.00000