HEADER LYASE 03-OCT-03 1R3Q TITLE UROPORPHYRINOGEN DECARBOXYLASE IN COMPLEX WITH COPROPORPHYRINOGEN-I COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROPORPHYRINOGEN DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: URO-D; UPD; COMPND 5 EC: 4.1.1.37; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS UROPORPHYRINOGEN DECARBOXYLASE COPROPORPHYRINOGEN; X-RAY KEYWDS 2 CRYSTALLOGRAPHY, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PHILLIPS,F.G.WHITBY,J.P.KUSHNER,C.P.HILL REVDAT 5 23-AUG-23 1R3Q 1 REMARK REVDAT 4 11-OCT-17 1R3Q 1 REMARK REVDAT 3 12-MAR-14 1R3Q 1 HETNAM REVDAT 2 24-FEB-09 1R3Q 1 VERSN REVDAT 1 09-DEC-03 1R3Q 0 JRNL AUTH J.D.PHILLIPS,F.G.WHITBY,J.P.KUSHNER,C.P.HILL JRNL TITL STRUCTURAL BASIS FOR TETRAPYRROLE COORDINATION BY JRNL TITL 2 UROPORPHYRINOGEN DECARBOXYLASE JRNL REF EMBO J. V. 22 6225 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 14633982 JRNL DOI 10.1093/EMBOJ/CDG606 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 87.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 48908 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1245 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7098 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 326 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.27000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : 1.90000 REMARK 3 B12 (A**2) : -0.63000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.724 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3012 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2762 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4106 ; 1.633 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6405 ; 0.884 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 5.412 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 432 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3414 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 633 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 680 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3279 ; 0.242 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1750 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 241 ; 0.191 ; 0.200 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): 14 ; 0.195 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 51 ; 0.337 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.136 ; 0.200 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): 1833 ; 1.042 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2952 ; 1.911 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1179 ; 2.976 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 5.000 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1R3Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50593 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 13.0000 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) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.48500 REMARK 200 R SYM FOR SHELL (I) : 0.48500 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1URO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION OF URO-D IN COMPLEX REMARK 280 WITH COPROPORPHYRINOGEN REQUIRED CRYSTALLIZATION IN AN ANAEROBIC REMARK 280 CHAMBER WITH PBG AND PBG-D ADDED TO THE SOLUTION FOR THE REMARK 280 GENERATION OF UROPORPHYRINOGEN IN-SITU. URO-D WAS ACTIVE UNDER REMARK 280 THESE CONDITIONS, CREATING COPROPORPHYRINOGEN. 1.5 M CITRATE, PH REMARK 280 6.5, LIQUID DIFFUSION, TEMPERATURE 294K 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 24.83667 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 49.67333 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 49.67333 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 24.83667 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS ONE URO-D MONOMER. URO-D IS A REMARK 300 DIMER. THE DIMER IS FORMED BY THE CRYSTALLOGRAPHIC 2-FOLD OPERATOR. 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 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 -0.500000 -0.866025 0.000000 51.46500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 89.13999 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 24.83667 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 4 REMARK 465 GLY A 5 REMARK 465 LEU A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 8 REMARK 465 GLN A 9 REMARK 465 ASN A 367 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 NH1 ARG A 249 O HOH A 4005 1.99 REMARK 500 OE2 GLU A 278 O HOH A 1288 2.05 REMARK 500 O LEU A 224 O HOH A 1280 2.08 REMARK 500 OH TYR A 202 O HOH A 1320 2.14 REMARK 500 O HOH A 1252 O HOH A 1254 2.16 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 ASP A 117 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 142 NE - CZ - NH1 ANGL. DEV. = 3.5 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 SER A 85 -157.55 -163.49 REMARK 500 ASN A 304 30.77 -143.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1CP A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO2 A 5001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1URO RELATED DB: PDB REMARK 900 UROPORPHYRINOGEN DECARBOXYLASE APO-ENZYME STRUCTURE REMARK 900 RELATED ID: 1R3R RELATED DB: PDB REMARK 900 RELATED ID: 1R3S RELATED DB: PDB REMARK 900 RELATED ID: 1R3T RELATED DB: PDB REMARK 900 RELATED ID: 1R3V RELATED DB: PDB REMARK 900 RELATED ID: 1R3W RELATED DB: PDB REMARK 900 RELATED ID: 1R3Y RELATED DB: PDB DBREF 1R3Q A 1 367 UNP P06132 DCUP_HUMAN 1 367 SEQRES 1 A 367 MET GLU ALA ASN GLY LEU GLY PRO GLN GLY PHE PRO GLU SEQRES 2 A 367 LEU LYS ASN ASP THR PHE LEU ARG ALA ALA TRP GLY GLU SEQRES 3 A 367 GLU THR ASP TYR THR PRO VAL TRP CYS MET ARG GLN ALA SEQRES 4 A 367 GLY ARG TYR LEU PRO GLU PHE ARG GLU THR ARG ALA ALA SEQRES 5 A 367 GLN ASP PHE PHE SER THR CYS ARG SER PRO GLU ALA CYS SEQRES 6 A 367 CYS GLU LEU THR LEU GLN PRO LEU ARG ARG PHE PRO LEU SEQRES 7 A 367 ASP ALA ALA ILE ILE PHE SER ASP ILE LEU VAL VAL PRO SEQRES 8 A 367 GLN ALA LEU GLY MET GLU VAL THR MET VAL PRO GLY LYS SEQRES 9 A 367 GLY PRO SER PHE PRO GLU PRO LEU ARG GLU GLU GLN ASP SEQRES 10 A 367 LEU GLU ARG LEU ARG ASP PRO GLU VAL VAL ALA SER GLU SEQRES 11 A 367 LEU GLY TYR VAL PHE GLN ALA ILE THR LEU THR ARG GLN SEQRES 12 A 367 ARG LEU ALA GLY ARG VAL PRO LEU ILE GLY PHE ALA GLY SEQRES 13 A 367 ALA PRO TRP THR LEU MET THR TYR MET VAL GLU GLY GLY SEQRES 14 A 367 GLY SER SER THR MET ALA GLN ALA LYS ARG TRP LEU TYR SEQRES 15 A 367 GLN ARG PRO GLN ALA SER HIS GLN LEU LEU ARG ILE LEU SEQRES 16 A 367 THR ASP ALA LEU VAL PRO TYR LEU VAL GLY GLN VAL VAL SEQRES 17 A 367 ALA GLY ALA GLN ALA LEU GLN LEU PHE GLU SER HIS ALA SEQRES 18 A 367 GLY HIS LEU GLY PRO GLN LEU PHE ASN LYS PHE ALA LEU SEQRES 19 A 367 PRO TYR ILE ARG ASP VAL ALA LYS GLN VAL LYS ALA ARG SEQRES 20 A 367 LEU ARG GLU ALA GLY LEU ALA PRO VAL PRO MET ILE ILE SEQRES 21 A 367 PHE ALA LYS ASP GLY HIS PHE ALA LEU GLU GLU LEU ALA SEQRES 22 A 367 GLN ALA GLY TYR GLU VAL VAL GLY LEU ASP TRP THR VAL SEQRES 23 A 367 ALA PRO LYS LYS ALA ARG GLU CYS VAL GLY LYS THR VAL SEQRES 24 A 367 THR LEU GLN GLY ASN LEU ASP PRO CYS ALA LEU TYR ALA SEQRES 25 A 367 SER GLU GLU GLU ILE GLY GLN LEU VAL LYS GLN MET LEU SEQRES 26 A 367 ASP ASP PHE GLY PRO HIS ARG TYR ILE ALA ASN LEU GLY SEQRES 27 A 367 HIS GLY LEU TYR PRO ASP MET ASP PRO GLU HIS VAL GLY SEQRES 28 A 367 ALA PHE VAL ASP ALA VAL HIS LYS HIS SER ARG LEU LEU SEQRES 29 A 367 ARG GLN ASN HET 1CP A 901 48 HET CO2 A5001 3 HETNAM 1CP COPROPORPHYRINOGEN I HETNAM CO2 CARBON DIOXIDE FORMUL 2 1CP C36 H44 N4 O8 FORMUL 3 CO2 C O2 FORMUL 4 HOH *326(H2 O) HELIX 1 1 ASP A 17 GLY A 25 1 9 HELIX 2 2 LEU A 43 ALA A 52 1 10 HELIX 3 3 ASP A 54 ARG A 60 1 7 HELIX 4 4 SER A 61 PHE A 76 1 16 HELIX 5 5 LEU A 88 LEU A 94 1 7 HELIX 6 6 GLU A 114 LEU A 121 5 8 HELIX 7 7 ASP A 123 GLU A 125 5 3 HELIX 8 8 VAL A 126 LEU A 131 1 6 HELIX 9 9 LEU A 131 ALA A 146 1 16 HELIX 10 10 ALA A 157 GLY A 168 1 12 HELIX 11 11 MET A 174 ARG A 184 1 11 HELIX 12 12 ARG A 184 ALA A 209 1 26 HELIX 13 13 HIS A 220 LEU A 224 5 5 HELIX 14 14 GLY A 225 ALA A 233 1 9 HELIX 15 15 ALA A 233 ALA A 251 1 19 HELIX 16 16 GLY A 265 PHE A 267 5 3 HELIX 17 17 ALA A 268 ALA A 273 1 6 HELIX 18 18 ALA A 287 GLY A 296 1 10 HELIX 19 19 ASP A 306 ALA A 312 5 7 HELIX 20 20 SER A 313 GLY A 329 1 17 HELIX 21 21 ASP A 346 LEU A 364 1 19 SHEET 1 A 7 ALA A 81 ILE A 82 0 SHEET 2 A 7 LEU A 151 GLY A 156 1 O ILE A 152 N ALA A 81 SHEET 3 A 7 ALA A 213 GLU A 218 1 O ALA A 213 N GLY A 153 SHEET 4 A 7 MET A 258 ALA A 262 1 O ILE A 259 N LEU A 216 SHEET 5 A 7 VAL A 279 GLY A 281 1 O GLY A 281 N ILE A 260 SHEET 6 A 7 THR A 300 LEU A 305 1 O THR A 300 N VAL A 280 SHEET 7 A 7 TYR A 333 LEU A 337 1 O ILE A 334 N LEU A 301 SHEET 1 B 2 THR A 99 VAL A 101 0 SHEET 2 B 2 GLY A 105 SER A 107 -1 O SER A 107 N THR A 99 CISPEP 1 GLY A 303 ASN A 304 0 -3.70 SITE 1 AC1 26 ARG A 37 GLN A 38 ALA A 39 ARG A 41 SITE 2 AC1 26 ARG A 50 PHE A 55 ILE A 82 ILE A 83 SITE 3 AC1 26 PHE A 84 SER A 85 ASP A 86 ILE A 87 SITE 4 AC1 26 PRO A 106 PHE A 154 TYR A 164 GLY A 170 SITE 5 AC1 26 PHE A 217 SER A 219 HIS A 339 HOH A1028 SITE 6 AC1 26 HOH A1111 HOH A1152 HOH A1164 HOH A1230 SITE 7 AC1 26 HOH A1286 CO2 A5001 SITE 1 AC2 3 ARG A 37 1CP A 901 HOH A1291 CRYST1 102.930 102.930 74.510 90.00 90.00 120.00 P 31 2 1 6 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 0.009715 0.005609 0.000000 0.00000 SCALE2 0.000000 0.011218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013421 0.00000