PDB Short entry for 1R3W HEADER LYASE 03-OCT-03 1R3W TITLE UROPORPHYRINOGEN DECARBOXYLASE Y164F MUTANT IN COMPLEX WITH TITLE 2 COPROPORPHYRINOGEN-III 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; COMPND 7 MUTATION: 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 1R3W 1 REMARK REVDAT 4 27-OCT-21 1R3W 1 REMARK SEQADV REVDAT 3 12-MAR-14 1R3W 1 HETNAM REVDAT 2 24-FEB-09 1R3W 1 VERSN REVDAT 1 09-DEC-03 1R3W 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 (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 47852 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1226 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) : 6873 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2797 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.01000 REMARK 3 B22 (A**2) : -1.01000 REMARK 3 B33 (A**2) : 1.51000 REMARK 3 B12 (A**2) : -0.50000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.780 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3101 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2831 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4243 ; 1.549 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6573 ; 0.911 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 389 ; 6.090 ; 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): 444 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3567 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 661 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 766 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3432 ; 0.244 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1763 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 252 ; 0.211 ; 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): 20 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 70 ; 0.328 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.151 ; 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): 1881 ; 0.922 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3047 ; 1.689 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1220 ; 2.597 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1196 ; 4.288 ; 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 1R3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49087 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 87.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : 0.39000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PBG, PBG-D AND U3S WERE ADDED TO THE REMARK 280 PROTEIN SOLUTION IN AN ANAEROBIC CHAMBER. URO-D WAS ACTIVE UNDER REMARK 280 THESE CONDITIONS, CONVERTING URO'GEN-III TO COP'GEN-III. 1.5 M REMARK 280 CITRATE, PH 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 24.54867 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 49.09733 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 49.09733 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 24.54867 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: URO-D IS A DIMER IN SOLUTION AND IN THE CRYSTAL. THE DIMER REMARK 300 IS FORMED BY THE 2-FOLD CRYSTALLOGRAPHIC ROTATION 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 51.51750 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 89.23093 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 24.54867 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 GLY A 10 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 O LEU A 224 O HOH A 1217 1.77 REMARK 500 N PHE A 11 O HOH A 1325 1.83 REMARK 500 O1M CP3 A 950 O HOH A 1306 2.02 REMARK 500 O HOH A 1105 O HOH A 1317 2.03 REMARK 500 OE2 GLU A 271 O HOH A 1196 2.05 REMARK 500 OE1 GLU A 271 O HOH A 1338 2.10 REMARK 500 O HOH A 1243 O HOH A 1253 2.11 REMARK 500 OD1 ASP A 239 NE2 GLN A 243 2.13 REMARK 500 O HOH A 1244 O HOH A 1268 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 79 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 239 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 239 CB - CG - OD2 ANGL. DEV. = 7.4 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 -161.79 -166.14 REMARK 500 PRO A 102 103.79 -52.48 REMARK 500 ASN A 304 31.39 -144.25 REMARK 500 HIS A 339 -179.35 -172.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 224 GLY A 225 146.91 REMARK 500 LEU A 224 GLY A 225 -140.35 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 CP3 A 950 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: 1R3Q RELATED DB: PDB 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: 1R3Y RELATED DB: PDB DBREF 1R3W A 1 367 UNP P06132 DCUP_HUMAN 1 367 SEQADV 1R3W PHE A 164 UNP P06132 TYR 164 ENGINEERED MUTATION 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 PHE 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 CP3 A 950 48 HETNAM CP3 COPROPORPHYRINOGEN III FORMUL 2 CP3 C36 H44 N4 O8 FORMUL 3 HOH *354(H2 O) HELIX 1 1 ASP A 17 TRP A 24 1 8 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 -5.74 SITE 1 AC1 22 ARG A 37 GLN A 38 ALA A 39 GLY A 40 SITE 2 AC1 22 ARG A 41 PHE A 46 PHE A 55 ILE A 82 SITE 3 AC1 22 ILE A 83 PHE A 84 SER A 85 ASP A 86 SITE 4 AC1 22 ILE A 87 MET A 100 PRO A 106 PHE A 154 SITE 5 AC1 22 GLY A 170 PHE A 217 SER A 219 HIS A 339 SITE 6 AC1 22 HOH A1166 HOH A1306 CRYST1 103.035 103.035 73.646 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 0.009705 0.005603 0.000000 0.00000 SCALE2 0.000000 0.011207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013578 0.00000