HEADER LYASE/LYASE INHIBITOR 16-SEP-11 3VI2 TITLE CRYSTAL STRUCTURE ANALYSIS OF PLASMODIUM FALCIPARUM OMP DECARBOXYLASE TITLE 2 IN COMPLEX WITH INHIBITOR HMOA COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: OROTIDINE 5 F-MONOPHOSPHATE DECARBOXYLASE; COMPND 5 EC: 4.1.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: OMPDC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OROTIDINE 5 F-MONOPHOSPHATE DECARBOXYLASE, LYASE-LYASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.TAKASHIMA,E.MIZOHATA,S.R.KRUNGKRAI,H.MATSUMURA,J.KRUNGKRAI,T.HORII, AUTHOR 2 T.INOUE REVDAT 3 20-MAR-24 3VI2 1 REMARK REVDAT 2 17-JUL-13 3VI2 1 JRNL REVDAT 1 01-AUG-12 3VI2 0 JRNL AUTH Y.TAKASHIMA,E.MIZOHATA,S.R.KRUNGKRAI,Y.FUKUNISHI, JRNL AUTH 2 T.KINOSHITA,T.SAKATA,H.MATSUMURA,J.KRUNGKRAI,T.HORII,T.INOUE JRNL TITL THE IN SILICO SCREENING AND X-RAY STRUCTURE ANALYSIS OF THE JRNL TITL 2 INHIBITOR COMPLEX OF PLASMODIUM FALCIPARUM OROTIDINE JRNL TITL 3 5'-MONOPHOSPHATE DECARBOXYLASE JRNL REF J.BIOCHEM. V. 152 133 2012 JRNL REFN ISSN 0021-924X JRNL PMID 22740703 JRNL DOI 10.1093/JB/MVS070 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 35421 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1864 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2439 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : -0.01000 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): 0.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.219 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.686 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5386 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7260 ; 1.837 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 8.060 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;40.652 ;25.652 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 992 ;20.055 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;24.103 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 772 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4092 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3170 ; 0.885 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5142 ; 1.481 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2216 ; 2.404 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2118 ; 3.410 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 318 REMARK 3 RESIDUE RANGE : A 500 A 500 REMARK 3 RESIDUE RANGE : A 324 A 324 REMARK 3 RESIDUE RANGE : A 325 A 395 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9607 33.2717 3.1259 REMARK 3 T TENSOR REMARK 3 T11: 0.3233 T22: 0.2096 REMARK 3 T33: 0.3047 T12: 0.0076 REMARK 3 T13: -0.1906 T23: -0.0315 REMARK 3 L TENSOR REMARK 3 L11: 3.9732 L22: 1.3638 REMARK 3 L33: 0.7592 L12: 0.5399 REMARK 3 L13: -0.4956 L23: 0.3265 REMARK 3 S TENSOR REMARK 3 S11: -0.6096 S12: -0.3011 S13: 0.6061 REMARK 3 S21: -0.0621 S22: 0.4123 S23: 0.1957 REMARK 3 S31: 0.1959 S32: 0.0627 S33: 0.1973 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 318 REMARK 3 RESIDUE RANGE : B 600 B 600 REMARK 3 RESIDUE RANGE : B 324 B 325 REMARK 3 RESIDUE RANGE : B 326 B 398 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5780 14.8071 -2.8564 REMARK 3 T TENSOR REMARK 3 T11: 0.3512 T22: 0.2497 REMARK 3 T33: 0.2464 T12: 0.0776 REMARK 3 T13: -0.0678 T23: -0.1678 REMARK 3 L TENSOR REMARK 3 L11: 1.6543 L22: 3.7258 REMARK 3 L33: 0.9338 L12: 0.0942 REMARK 3 L13: 0.0380 L23: 0.3626 REMARK 3 S TENSOR REMARK 3 S11: -0.4939 S12: -0.0286 S13: -0.0817 REMARK 3 S21: 0.2374 S22: 0.5383 S23: -0.4953 REMARK 3 S31: 0.3110 S32: 0.2034 S33: -0.0444 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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. THE STRUCTURE WAS REFINED ALSO WITH CNS1.2 REMARK 4 REMARK 4 3VI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BL38B1 FIXED EXIT SI 111 DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, 27% PEGMME 2K, 3% 1,6 REMARK 280 -HEXANDIOL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 100.98500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 58.30372 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.76000 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 100.98500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 58.30372 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.76000 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 100.98500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 58.30372 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.76000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 116.60743 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 29.52000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 116.60743 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 29.52000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 116.60743 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 29.52000 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: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 GLN A 319 REMARK 465 ASN A 320 REMARK 465 MET A 321 REMARK 465 GLU A 322 REMARK 465 SER A 323 REMARK 465 GLN B 319 REMARK 465 ASN B 320 REMARK 465 MET B 321 REMARK 465 GLU B 322 REMARK 465 SER B 323 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 351 O HOH A 383 1.98 REMARK 500 O HIS A 274 N THR A 276 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 122 CB VAL A 122 CG2 0.140 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 PRO A 67 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG B 150 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU B 230 CA - CB - CG ANGL. DEV. = 14.9 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 LYS A 37 13.13 -58.34 REMARK 500 GLU A 38 -49.74 -133.42 REMARK 500 ALA A 66 121.39 -23.13 REMARK 500 PRO A 67 -54.69 -20.32 REMARK 500 ASP A 68 -150.86 -67.90 REMARK 500 GLU A 73 -90.44 32.45 REMARK 500 ASP A 141 -168.63 -177.99 REMARK 500 VAL A 192 -67.54 -122.90 REMARK 500 ASN A 210 -2.96 66.91 REMARK 500 SER A 245 73.64 -105.17 REMARK 500 PRO A 257 171.67 -52.08 REMARK 500 ASN A 258 -6.37 59.51 REMARK 500 ASN A 270 -155.52 -83.18 REMARK 500 LYS A 275 -8.76 -29.48 REMARK 500 THR A 276 -12.74 156.71 REMARK 500 TYR A 281 30.70 83.45 REMARK 500 LYS A 283 -143.10 -160.84 REMARK 500 PRO A 300 -36.61 -32.92 REMARK 500 LEU A 317 35.86 -70.08 REMARK 500 PRO B 67 64.90 -67.37 REMARK 500 ASP B 68 41.65 -101.72 REMARK 500 ILE B 70 -79.12 -56.67 REMARK 500 ARG B 72 75.99 -103.53 REMARK 500 GLU B 73 -120.20 44.27 REMARK 500 GLU B 74 35.99 29.14 REMARK 500 LYS B 204 -59.16 -130.97 REMARK 500 ASP B 209 61.27 -160.85 REMARK 500 ASN B 258 -9.32 59.57 REMARK 500 ASN B 270 -107.63 27.27 REMARK 500 HIS B 274 35.09 -94.50 REMARK 500 HIS B 282 -123.35 -164.33 REMARK 500 LYS B 283 130.25 -35.68 REMARK 500 ASN B 314 6.55 -66.63 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 ASN A 270 GLY A 271 -54.30 REMARK 500 SER A 284 TYR A 285 -135.76 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 HMZ A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HMZ B 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 324 DBREF 3VI2 A 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 DBREF 3VI2 B 1 323 UNP Q8T6J6 Q8T6J6_PLAFA 1 323 SEQRES 1 A 323 MET GLY PHE LYS VAL LYS LEU GLU LYS ARG ARG ASN ALA SEQRES 2 A 323 ILE ASN THR CYS LEU CYS ILE GLY LEU ASP PRO ASP GLU SEQRES 3 A 323 LYS ASP ILE GLU ASN PHE MET LYS ASN GLU LYS GLU ASN SEQRES 4 A 323 ASN TYR ASN ASN ILE LYS LYS ASN LEU LYS GLU LYS TYR SEQRES 5 A 323 ILE ASN ASN VAL SER ILE LYS LYS ASP ILE LEU LEU LYS SEQRES 6 A 323 ALA PRO ASP ASN ILE ILE ARG GLU GLU LYS SER GLU GLU SEQRES 7 A 323 PHE PHE TYR PHE PHE ASN HIS PHE CYS PHE TYR ILE ILE SEQRES 8 A 323 ASN GLU THR ASN LYS TYR ALA LEU THR PHE LYS MET ASN SEQRES 9 A 323 PHE ALA PHE TYR ILE PRO TYR GLY SER VAL GLY ILE ASP SEQRES 10 A 323 VAL LEU LYS ASN VAL PHE ASP TYR LEU TYR GLU LEU ASN SEQRES 11 A 323 ILE PRO THR ILE LEU ASP MET LYS ILE ASN ASP ILE GLY SEQRES 12 A 323 ASN THR VAL LYS ASN TYR ARG LYS PHE ILE PHE GLU TYR SEQRES 13 A 323 LEU LYS SER ASP SER CYS THR VAL ASN ILE TYR MET GLY SEQRES 14 A 323 THR ASN MET LEU LYS ASP ILE CYS TYR ASP GLU GLU LYS SEQRES 15 A 323 ASN LYS TYR TYR SER ALA PHE VAL LEU VAL LYS THR THR SEQRES 16 A 323 ASN PRO ASP SER ALA ILE PHE GLN LYS ASN LEU SER LEU SEQRES 17 A 323 ASP ASN LYS GLN ALA TYR VAL ILE MET ALA GLN GLU ALA SEQRES 18 A 323 LEU ASN MET SER SER TYR LEU ASN LEU GLU GLN ASN ASN SEQRES 19 A 323 GLU PHE ILE GLY PHE VAL VAL GLY ALA ASN SER TYR ASP SEQRES 20 A 323 GLU MET ASN TYR ILE ARG THR TYR PHE PRO ASN CYS TYR SEQRES 21 A 323 ILE LEU SER PRO GLY ILE GLY ALA GLN ASN GLY ASP LEU SEQRES 22 A 323 HIS LYS THR LEU THR ASN GLY TYR HIS LYS SER TYR GLU SEQRES 23 A 323 LYS ILE LEU ILE ASN ILE GLY ARG ALA ILE THR LYS ASN SEQRES 24 A 323 PRO TYR PRO GLN LYS ALA ALA GLN MET TYR TYR ASP GLN SEQRES 25 A 323 ILE ASN ALA ILE LEU LYS GLN ASN MET GLU SER SEQRES 1 B 323 MET GLY PHE LYS VAL LYS LEU GLU LYS ARG ARG ASN ALA SEQRES 2 B 323 ILE ASN THR CYS LEU CYS ILE GLY LEU ASP PRO ASP GLU SEQRES 3 B 323 LYS ASP ILE GLU ASN PHE MET LYS ASN GLU LYS GLU ASN SEQRES 4 B 323 ASN TYR ASN ASN ILE LYS LYS ASN LEU LYS GLU LYS TYR SEQRES 5 B 323 ILE ASN ASN VAL SER ILE LYS LYS ASP ILE LEU LEU LYS SEQRES 6 B 323 ALA PRO ASP ASN ILE ILE ARG GLU GLU LYS SER GLU GLU SEQRES 7 B 323 PHE PHE TYR PHE PHE ASN HIS PHE CYS PHE TYR ILE ILE SEQRES 8 B 323 ASN GLU THR ASN LYS TYR ALA LEU THR PHE LYS MET ASN SEQRES 9 B 323 PHE ALA PHE TYR ILE PRO TYR GLY SER VAL GLY ILE ASP SEQRES 10 B 323 VAL LEU LYS ASN VAL PHE ASP TYR LEU TYR GLU LEU ASN SEQRES 11 B 323 ILE PRO THR ILE LEU ASP MET LYS ILE ASN ASP ILE GLY SEQRES 12 B 323 ASN THR VAL LYS ASN TYR ARG LYS PHE ILE PHE GLU TYR SEQRES 13 B 323 LEU LYS SER ASP SER CYS THR VAL ASN ILE TYR MET GLY SEQRES 14 B 323 THR ASN MET LEU LYS ASP ILE CYS TYR ASP GLU GLU LYS SEQRES 15 B 323 ASN LYS TYR TYR SER ALA PHE VAL LEU VAL LYS THR THR SEQRES 16 B 323 ASN PRO ASP SER ALA ILE PHE GLN LYS ASN LEU SER LEU SEQRES 17 B 323 ASP ASN LYS GLN ALA TYR VAL ILE MET ALA GLN GLU ALA SEQRES 18 B 323 LEU ASN MET SER SER TYR LEU ASN LEU GLU GLN ASN ASN SEQRES 19 B 323 GLU PHE ILE GLY PHE VAL VAL GLY ALA ASN SER TYR ASP SEQRES 20 B 323 GLU MET ASN TYR ILE ARG THR TYR PHE PRO ASN CYS TYR SEQRES 21 B 323 ILE LEU SER PRO GLY ILE GLY ALA GLN ASN GLY ASP LEU SEQRES 22 B 323 HIS LYS THR LEU THR ASN GLY TYR HIS LYS SER TYR GLU SEQRES 23 B 323 LYS ILE LEU ILE ASN ILE GLY ARG ALA ILE THR LYS ASN SEQRES 24 B 323 PRO TYR PRO GLN LYS ALA ALA GLN MET TYR TYR ASP GLN SEQRES 25 B 323 ILE ASN ALA ILE LEU LYS GLN ASN MET GLU SER HET HMZ A 500 16 HET NA A 324 1 HET HMZ B 600 16 HET NA B 324 1 HET NA B 325 1 HETNAM HMZ 4-(2-HYDROXY-4-METHOXYPHENYL)-4-OXOBUTANOIC ACID HETNAM NA SODIUM ION FORMUL 3 HMZ 2(C11 H12 O5) FORMUL 4 NA 3(NA 1+) FORMUL 8 HOH *108(H2 O) HELIX 1 1 GLY A 2 ASN A 15 1 14 HELIX 2 2 ASP A 25 ASN A 40 1 16 HELIX 3 3 TYR A 41 LEU A 48 1 8 HELIX 4 4 GLU A 50 VAL A 56 5 7 HELIX 5 5 LYS A 59 LEU A 64 1 6 HELIX 6 6 GLU A 77 ASN A 95 1 19 HELIX 7 7 LYS A 96 ALA A 98 5 3 HELIX 8 8 ALA A 106 ILE A 109 5 4 HELIX 9 9 GLY A 112 LEU A 129 1 18 HELIX 10 10 ILE A 142 GLU A 155 1 14 HELIX 11 11 ILE A 166 GLY A 169 5 4 HELIX 12 12 THR A 170 ILE A 176 5 7 HELIX 13 13 GLU A 180 ASN A 183 5 4 HELIX 14 14 SER A 199 LYS A 204 1 6 HELIX 15 15 ALA A 213 LEU A 228 1 16 HELIX 16 16 SER A 245 PHE A 256 1 12 HELIX 17 17 SER A 284 GLU A 286 5 3 HELIX 18 18 GLY A 293 LYS A 298 1 6 HELIX 19 19 TYR A 301 LEU A 317 1 17 HELIX 20 20 GLY B 2 ASN B 15 1 14 HELIX 21 21 ASP B 25 GLU B 38 1 14 HELIX 22 22 TYR B 41 GLU B 50 1 10 HELIX 23 23 LYS B 51 VAL B 56 5 6 HELIX 24 24 LYS B 59 LEU B 64 1 6 HELIX 25 25 GLU B 74 SER B 76 5 3 HELIX 26 26 GLU B 77 ASN B 95 1 19 HELIX 27 27 ALA B 106 ILE B 109 5 4 HELIX 28 28 SER B 113 LEU B 129 1 17 HELIX 29 29 ILE B 142 GLU B 155 1 14 HELIX 30 30 ILE B 166 ASP B 175 5 10 HELIX 31 31 SER B 199 LYS B 204 1 6 HELIX 32 32 GLN B 212 LEU B 228 1 17 HELIX 33 33 SER B 245 PHE B 256 1 12 HELIX 34 34 SER B 284 GLU B 286 5 3 HELIX 35 35 GLY B 293 LYS B 298 1 6 HELIX 36 36 TYR B 301 LEU B 317 1 17 SHEET 1 A 9 LEU A 18 LEU A 22 0 SHEET 2 A 9 THR A 100 ASN A 104 1 O LYS A 102 N LEU A 22 SHEET 3 A 9 THR A 133 ILE A 139 1 O ASP A 136 N MET A 103 SHEET 4 A 9 SER A 161 VAL A 164 1 O SER A 161 N LEU A 135 SHEET 5 A 9 SER A 187 LYS A 193 1 O PHE A 189 N CYS A 162 SHEET 6 A 9 ILE A 237 VAL A 241 1 O VAL A 240 N VAL A 190 SHEET 7 A 9 ILE A 261 ILE A 266 1 O LEU A 262 N PHE A 239 SHEET 8 A 9 ILE A 288 ILE A 292 1 O LEU A 289 N ILE A 261 SHEET 9 A 9 LEU A 18 LEU A 22 1 N CYS A 19 O ILE A 292 SHEET 1 B 2 TYR A 178 ASP A 179 0 SHEET 2 B 2 LYS A 184 TYR A 185 -1 O LYS A 184 N ASP A 179 SHEET 1 C 2 SER A 207 LEU A 208 0 SHEET 2 C 2 LYS A 211 GLN A 212 -1 O LYS A 211 N LEU A 208 SHEET 1 D 9 LEU B 18 LEU B 22 0 SHEET 2 D 9 THR B 100 ASN B 104 1 O LYS B 102 N LEU B 22 SHEET 3 D 9 THR B 133 ILE B 139 1 O ILE B 134 N MET B 103 SHEET 4 D 9 CYS B 162 VAL B 164 1 O THR B 163 N LEU B 135 SHEET 5 D 9 ALA B 188 LYS B 193 1 O PHE B 189 N VAL B 164 SHEET 6 D 9 ILE B 237 VAL B 241 1 O GLY B 238 N ALA B 188 SHEET 7 D 9 ILE B 261 PRO B 264 1 O LEU B 262 N PHE B 239 SHEET 8 D 9 ILE B 288 ILE B 292 1 O LEU B 289 N SER B 263 SHEET 9 D 9 LEU B 18 LEU B 22 1 N CYS B 19 O ILE B 292 SHEET 1 E 2 TYR B 178 ASP B 179 0 SHEET 2 E 2 LYS B 184 TYR B 185 -1 O LYS B 184 N ASP B 179 SITE 1 AC1 11 ASP A 23 LYS A 102 THR A 195 ILE A 266 SITE 2 AC1 11 ALA A 268 GLN A 269 ASN A 291 GLY A 293 SITE 3 AC1 11 ARG A 294 HOH A 390 ILE B 142 SITE 1 AC2 11 GLY B 21 ASP B 23 THR B 195 GLY B 265 SITE 2 AC2 11 ILE B 266 ALA B 268 GLN B 269 ASN B 291 SITE 3 AC2 11 GLY B 293 ARG B 294 HOH B 364 SITE 1 AC3 1 ASN A 15 CRYST1 201.970 201.970 44.280 90.00 90.00 120.00 H 3 18 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 0.004951 0.002859 0.000000 0.00000 SCALE2 0.000000 0.005717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022584 0.00000