HEADER BIOSYNTHETIC PROTEIN 21-AUG-18 6HFI TITLE HUMAN DIHYDROOROTASE MUTANT F1563A APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAD PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.5.5,2.1.3.2,3.5.2.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CAD; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293 GNTI; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPIN-M KEYWDS DE NOVO PYRIMIDINE BIOSYNTHESIS, CAD, TIM-BARREL, CARBOXYLATED KEYWDS 2 LYSINE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,A.GRANDE GARCIA REVDAT 3 17-JAN-24 6HFI 1 LINK REVDAT 2 19-DEC-18 6HFI 1 JRNL REVDAT 1 24-OCT-18 6HFI 0 JRNL AUTH F.DEL CANO-OCHOA,A.GRANDE-GARCIA,M.REVERTE-LOPEZ,M.D'ABRAMO, JRNL AUTH 2 S.RAMON-MAIQUES JRNL TITL CHARACTERIZATION OF THE CATALYTIC FLEXIBLE LOOP IN THE JRNL TITL 2 DIHYDROOROTASE DOMAIN OF THE HUMAN MULTI-ENZYMATIC PROTEIN JRNL TITL 3 CAD. JRNL REF J. BIOL. CHEM. V. 293 18903 2018 JRNL REFN ESSN 1083-351X JRNL PMID 30315107 JRNL DOI 10.1074/JBC.RA118.005494 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.992 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 132840 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.003 REMARK 3 FREE R VALUE TEST SET COUNT : 6646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.2507 - 4.5304 0.99 4221 228 0.1540 0.1676 REMARK 3 2 4.5304 - 3.5982 0.98 4156 223 0.1149 0.1373 REMARK 3 3 3.5982 - 3.1441 0.99 4256 230 0.1228 0.1506 REMARK 3 4 3.1441 - 2.8569 1.00 4241 225 0.1312 0.1794 REMARK 3 5 2.8569 - 2.6523 1.00 4221 211 0.1281 0.1646 REMARK 3 6 2.6523 - 2.4960 1.00 4249 228 0.1134 0.1523 REMARK 3 7 2.4960 - 2.3711 1.00 4221 220 0.1043 0.1293 REMARK 3 8 2.3711 - 2.2679 1.00 4215 220 0.1129 0.1441 REMARK 3 9 2.2679 - 2.1806 0.93 3963 214 0.1300 0.2052 REMARK 3 10 2.1806 - 2.1054 1.00 4261 223 0.1028 0.1530 REMARK 3 11 2.1054 - 2.0396 0.99 4188 221 0.1060 0.1716 REMARK 3 12 2.0396 - 1.9813 1.00 4254 222 0.1158 0.1393 REMARK 3 13 1.9813 - 1.9292 0.98 4184 218 0.1247 0.1574 REMARK 3 14 1.9292 - 1.8821 0.91 3929 207 0.1733 0.2366 REMARK 3 15 1.8821 - 1.8393 1.00 4210 224 0.1061 0.1309 REMARK 3 16 1.8393 - 1.8002 1.00 4209 223 0.1027 0.1517 REMARK 3 17 1.8002 - 1.7642 1.00 4257 224 0.1088 0.1623 REMARK 3 18 1.7642 - 1.7309 1.00 4276 223 0.1106 0.1530 REMARK 3 19 1.7309 - 1.7000 1.00 4209 222 0.1181 0.1593 REMARK 3 20 1.7000 - 1.6712 1.00 4273 224 0.1200 0.1591 REMARK 3 21 1.6712 - 1.6442 1.00 4240 222 0.1293 0.1870 REMARK 3 22 1.6442 - 1.6189 1.00 4203 226 0.1422 0.1675 REMARK 3 23 1.6189 - 1.5951 1.00 4270 226 0.1440 0.1789 REMARK 3 24 1.5951 - 1.5727 1.00 4201 220 0.1461 0.1913 REMARK 3 25 1.5727 - 1.5514 1.00 4255 222 0.1588 0.2095 REMARK 3 26 1.5514 - 1.5313 1.00 4287 220 0.1674 0.2119 REMARK 3 27 1.5313 - 1.5121 0.99 4204 221 0.1727 0.1928 REMARK 3 28 1.5121 - 1.4939 1.00 4239 224 0.1852 0.2151 REMARK 3 29 1.4939 - 1.4765 0.99 4223 220 0.2517 0.2648 REMARK 3 30 1.4765 - 1.4599 0.97 4079 215 0.2857 0.3156 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.123 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.085 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 3004 REMARK 3 ANGLE : 1.302 4116 REMARK 3 CHIRALITY : 0.225 461 REMARK 3 PLANARITY : 0.009 546 REMARK 3 DIHEDRAL : 26.155 1134 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6HFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011170. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-14 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 132840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 79.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 4C6C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 2-3 MG/ML IN 20 MM TRIS PH REMARK 280 8, 0.15 M NACL, 0.02 MM ZINC SULFATE, 0.2 MM TCEP MOTHER LIQUOR: REMARK 280 2.5-3 M POTASSIUM FORMATE, 0.1 M HEPES PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 30.65000 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 30.65000 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 40.90000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.54500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.54500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.65000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.54500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.65000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.90000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.54500 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: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -320.0 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 -30.65000 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 A2323 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2343 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2352 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 1454 REMARK 465 PRO A 1455 REMARK 465 MET A 1456 REMARK 465 THR A 1457 REMARK 465 SER A 1458 REMARK 465 GLN A 1459 REMARK 465 PRO A 1822 REMARK 465 SER A 1823 REMARK 465 ALA A 1824 REMARK 465 PRO A 1825 REMARK 465 ALA A 1826 REMARK 465 THR A 1827 REMARK 465 SER A 1828 REMARK 465 GLU A 1829 REMARK 465 MET A 1830 REMARK 465 THR A 1831 REMARK 465 THR A 1832 REMARK 465 THR A 1833 REMARK 465 PRO A 1834 REMARK 465 GLU A 1835 REMARK 465 ARG A 1836 REMARK 465 PRO A 1837 REMARK 465 ARG A 1838 REMARK 465 ARG A 1839 REMARK 465 GLY A 1840 REMARK 465 ILE A 1841 REMARK 465 PRO A 1842 REMARK 465 GLY A 1843 REMARK 465 LEU A 1844 REMARK 465 PRO A 1845 REMARK 465 ASP A 1846 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 LYS A1460 CG CD CE NZ 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 2008 O HOH A 2061 2.06 REMARK 500 O HOH A 2290 O HOH A 2339 2.10 REMARK 500 O HOH A 2264 O HOH A 2349 2.17 REMARK 500 OG SER A 1719 O HOH A 2001 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HG CYS A 1696 HG CYS A 1696 3454 0.89 REMARK 500 SG CYS A 1696 HG CYS A 1696 3454 1.41 REMARK 500 O HOH A 2008 O HOH A 2269 3554 2.05 REMARK 500 O HOH A 2234 O HOH A 2370 3554 2.18 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 LEU A1566 CB - CG - CD2 ANGL. DEV. = 11.7 DEGREES REMARK 500 CYS A1613 CA - CB - SG ANGL. DEV. = 7.6 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 ARG A1475 -1.64 68.57 REMARK 500 GLU A1483 156.34 176.03 REMARK 500 ASN A1505 44.81 -83.72 REMARK 500 ASN A1560 -169.67 -110.88 REMARK 500 GLU A1565 2.07 -63.53 REMARK 500 GLN A1593 -123.14 51.49 REMARK 500 HIS A1614 76.04 22.08 REMARK 500 HIS A1733 -69.88 -146.69 REMARK 500 ASP A1796 54.49 39.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 NE2 REMARK 620 2 HIS A1473 NE2 115.2 REMARK 620 3 KCX A1556 OQ2 92.8 92.6 REMARK 620 4 ASP A1686 OD1 83.0 89.1 175.9 REMARK 620 5 HOH A2153 O 116.7 127.6 91.6 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1903 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1471 ND1 REMARK 620 2 CYS A1613 SG 117.6 REMARK 620 3 GLU A1637 OE1 82.7 116.0 REMARK 620 4 HOH A2167 O 120.0 108.5 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A1556 OQ1 REMARK 620 2 HIS A1590 ND1 106.2 REMARK 620 3 HIS A1614 NE2 110.4 93.3 REMARK 620 4 HOH A2153 O 106.7 130.0 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1909 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1734 NE2 REMARK 620 2 HOH A2297 O 111.7 REMARK 620 3 HOH A2307 O 109.6 86.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 1908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1909 DBREF 6HFI A 1456 1846 UNP P27708 PYR1_HUMAN 1456 1846 SEQADV 6HFI GLY A 1454 UNP P27708 EXPRESSION TAG SEQADV 6HFI PRO A 1455 UNP P27708 EXPRESSION TAG SEQADV 6HFI ALA A 1563 UNP P27708 PHE 1563 ENGINEERED MUTATION SEQRES 1 A 393 GLY PRO MET THR SER GLN LYS LEU VAL ARG LEU PRO GLY SEQRES 2 A 393 LEU ILE ASP VAL HIS VAL HIS LEU ARG GLU PRO GLY GLY SEQRES 3 A 393 THR HIS LYS GLU ASP PHE ALA SER GLY THR ALA ALA ALA SEQRES 4 A 393 LEU ALA GLY GLY ILE THR MET VAL CYS ALA MET PRO ASN SEQRES 5 A 393 THR ARG PRO PRO ILE ILE ASP ALA PRO ALA LEU ALA LEU SEQRES 6 A 393 ALA GLN LYS LEU ALA GLU ALA GLY ALA ARG CYS ASP PHE SEQRES 7 A 393 ALA LEU PHE LEU GLY ALA SER SER GLU ASN ALA GLY THR SEQRES 8 A 393 LEU GLY THR VAL ALA GLY SER ALA ALA GLY LEU KCX LEU SEQRES 9 A 393 TYR LEU ASN GLU THR ALA SER GLU LEU ARG LEU ASP SER SEQRES 10 A 393 VAL VAL GLN TRP MET GLU HIS PHE GLU THR TRP PRO SER SEQRES 11 A 393 HIS LEU PRO ILE VAL ALA HIS ALA GLU GLN GLN THR VAL SEQRES 12 A 393 ALA ALA VAL LEU MET VAL ALA GLN LEU THR GLN ARG SER SEQRES 13 A 393 VAL HIS ILE CYS HIS VAL ALA ARG LYS GLU GLU ILE LEU SEQRES 14 A 393 LEU ILE LYS ALA ALA LYS ALA ARG GLY LEU PRO VAL THR SEQRES 15 A 393 CYS GLU VAL ALA PRO HIS HIS LEU PHE LEU SER HIS ASP SEQRES 16 A 393 ASP LEU GLU ARG LEU GLY PRO GLY LYS GLY GLU VAL ARG SEQRES 17 A 393 PRO GLU LEU GLY SER ARG GLN ASP VAL GLU ALA LEU TRP SEQRES 18 A 393 GLU ASN MET ALA VAL ILE ASP CYS PHE ALA SER ASP HIS SEQRES 19 A 393 ALA PRO HIS THR LEU GLU GLU LYS CYS GLY SER ARG PRO SEQRES 20 A 393 PRO PRO GLY PHE PRO GLY LEU GLU THR MET LEU PRO LEU SEQRES 21 A 393 LEU LEU THR ALA VAL SER GLU GLY ARG LEU SER LEU ASP SEQRES 22 A 393 ASP LEU LEU GLN ARG LEU HIS HIS ASN PRO ARG ARG ILE SEQRES 23 A 393 PHE HIS LEU PRO PRO GLN GLU ASP THR TYR VAL GLU VAL SEQRES 24 A 393 ASP LEU GLU HIS GLU TRP THR ILE PRO SER HIS MET PRO SEQRES 25 A 393 PHE SER LYS ALA HIS TRP THR PRO PHE GLU GLY GLN LYS SEQRES 26 A 393 VAL LYS GLY THR VAL ARG ARG VAL VAL LEU ARG GLY GLU SEQRES 27 A 393 VAL ALA TYR ILE ASP GLY GLN VAL LEU VAL PRO PRO GLY SEQRES 28 A 393 TYR GLY GLN ASP VAL ARG LYS TRP PRO GLN GLY ALA VAL SEQRES 29 A 393 PRO GLN LEU PRO PRO SER ALA PRO ALA THR SER GLU MET SEQRES 30 A 393 THR THR THR PRO GLU ARG PRO ARG ARG GLY ILE PRO GLY SEQRES 31 A 393 LEU PRO ASP MODRES 6HFI KCX A 1556 LYS MODIFIED RESIDUE HET KCX A1556 23 HET ZN A1901 1 HET ZN A1902 1 HET ZN A1903 1 HET FMT A1904 4 HET FMT A1905 4 HET FMT A1906 4 HET FMT A1907 4 HET FMT A1908 4 HET ZN A1909 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM ZN ZINC ION HETNAM FMT FORMIC ACID FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 ZN 4(ZN 2+) FORMUL 5 FMT 5(C H2 O2) FORMUL 11 HOH *385(H2 O) HELIX 1 AA1 ASP A 1484 GLY A 1495 1 12 HELIX 2 AA2 ASP A 1512 ALA A 1527 1 16 HELIX 3 AA3 VAL A 1548 ALA A 1552 5 5 HELIX 4 AA4 SER A 1570 TRP A 1581 1 12 HELIX 5 AA5 GLN A 1593 THR A 1606 1 14 HELIX 6 AA6 ARG A 1617 ARG A 1630 1 14 HELIX 7 AA7 ALA A 1639 LEU A 1645 1 7 HELIX 8 AA8 SER A 1646 ASP A 1648 5 3 HELIX 9 AA9 ASP A 1649 GLY A 1658 1 10 HELIX 10 AB1 SER A 1666 ASN A 1676 1 11 HELIX 11 AB2 MET A 1677 ILE A 1680 5 4 HELIX 12 AB3 THR A 1691 CYS A 1696 1 6 HELIX 13 AB4 GLY A 1706 GLU A 1720 1 15 HELIX 14 AB5 SER A 1724 HIS A 1733 1 10 HELIX 15 AB6 HIS A 1733 HIS A 1741 1 9 HELIX 16 AB7 ASP A 1808 ALA A 1816 5 9 SHEET 1 AA1 5 VAL A1462 PRO A1465 0 SHEET 2 AA1 5 TYR A1749 THR A1759 -1 O VAL A1750 N LEU A1464 SHEET 3 AA1 5 LYS A1778 LEU A1788 -1 O ARG A1785 N GLU A1751 SHEET 4 AA1 5 GLU A1791 ILE A1795 -1 O ALA A1793 N VAL A1786 SHEET 5 AA1 5 GLN A1798 VAL A1799 -1 O GLN A1798 N ILE A1795 SHEET 1 AA2 3 LEU A1467 VAL A1472 0 SHEET 2 AA2 3 ILE A1497 ALA A1502 1 O THR A1498 N LEU A1467 SHEET 3 AA2 3 ASP A1530 LEU A1533 1 O ALA A1532 N ALA A1502 SHEET 1 AA3 6 LEU A1535 GLY A1536 0 SHEET 2 AA3 6 LEU A1555 TYR A1558 1 O KCX A1556 N LEU A1535 SHEET 3 AA3 6 ILE A1587 HIS A1590 1 O VAL A1588 N LEU A1555 SHEET 4 AA3 6 VAL A1610 ILE A1612 1 O HIS A1611 N ALA A1589 SHEET 5 AA3 6 VAL A1634 VAL A1638 1 O THR A1635 N ILE A1612 SHEET 6 AA3 6 CYS A1682 PHE A1683 1 O CYS A1682 N VAL A1638 SSBOND 1 CYS A 1696 CYS A 1696 1555 3454 2.15 LINK C LEU A1555 N KCX A1556 1555 1555 1.34 LINK C KCX A1556 N LEU A1557 1555 1555 1.33 LINK NE2 HIS A1471 ZN ZN A1902 1555 1555 2.01 LINK ND1 HIS A1471 ZN ZN A1903 1555 1555 2.06 LINK NE2 HIS A1473 ZN ZN A1902 1555 1555 2.03 LINK OQ1 KCX A1556 ZN ZN A1901 1555 1555 1.88 LINK OQ2 KCX A1556 ZN ZN A1902 1555 1555 2.13 LINK ND1 HIS A1590 ZN ZN A1901 1555 1555 2.04 LINK SG ACYS A1613 ZN ZN A1903 1555 1555 2.36 LINK NE2 HIS A1614 ZN ZN A1901 1555 1555 2.01 LINK OE1 GLU A1637 ZN ZN A1903 1555 1555 2.21 LINK OD1 ASP A1686 ZN ZN A1902 1555 1555 2.25 LINK NE2 HIS A1734 ZN ZN A1909 1555 1555 2.18 LINK ZN ZN A1901 O HOH A2153 1555 1555 1.96 LINK ZN ZN A1902 O HOH A2153 1555 1555 2.00 LINK ZN ZN A1903 O HOH A2167 1555 1555 2.16 LINK ZN ZN A1909 O HOH A2297 1555 1555 2.04 LINK ZN ZN A1909 O HOH A2307 1555 1555 2.21 CISPEP 1 GLU A 1476 PRO A 1477 0 7.31 CISPEP 2 ARG A 1507 PRO A 1508 0 1.24 CISPEP 3 ARG A 1661 PRO A 1662 0 -6.18 SITE 1 AC1 5 KCX A1556 HIS A1590 HIS A1614 ZN A1902 SITE 2 AC1 5 HOH A2153 SITE 1 AC2 6 HIS A1471 HIS A1473 KCX A1556 ASP A1686 SITE 2 AC2 6 ZN A1901 HOH A2153 SITE 1 AC3 5 HIS A1471 MET A1503 CYS A1613 GLU A1637 SITE 2 AC3 5 HOH A2167 SITE 1 AC4 8 PRO A1586 ILE A1587 ARG A1608 SER A1609 SITE 2 AC4 8 VAL A1610 HIS A1611 HOH A2056 HOH A2187 SITE 1 AC5 2 HIS A1734 ARG A1737 SITE 1 AC6 5 ARG A1463 THR A1748 GLN A1814 HOH A2010 SITE 2 AC6 5 HOH A2233 SITE 1 AC7 5 HIS A1473 ARG A1475 ASN A1505 HIS A1690 SITE 2 AC7 5 PRO A1702 SITE 1 AC8 4 GLN A1604 LEU A1605 ARG A1630 HOH A2082 SITE 1 AC9 4 HIS A1734 HIS A1741 HOH A2297 HOH A2307 CRYST1 81.800 159.090 61.300 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 0.012225 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016313 0.00000