HEADER HYDROLASE 02-AUG-23 8Q2E TITLE THE 1.68-A X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE TITLE 2 INHIBITED BY THIRAM AND BOUND TO DIMETHYLDITIOCARBAMATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREASE SUBUNIT GAMMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UREA AMIDOHYDROLASE SUBUNIT GAMMA; COMPND 5 EC: 3.5.1.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UREASE SUBUNIT BETA; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: UREA AMIDOHYDROLASE SUBUNIT BETA; COMPND 10 EC: 3.5.1.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: UREASE SUBUNIT ALPHA; COMPND 13 CHAIN: C; COMPND 14 SYNONYM: UREA AMIDOHYDROLASE SUBUNIT ALPHA; COMPND 15 EC: 3.5.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 3 ORGANISM_TAXID: 1474; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 6 ORGANISM_TAXID: 1474; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 9 ORGANISM_TAXID: 1474 KEYWDS UREASE, NICKEL, THIRAM, DIMETHYLDITHIOCARBAMATE, ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MAZZEI,M.CIANCI,S.CIURLI REVDAT 2 15-NOV-23 8Q2E 1 REMARK REVDAT 1 01-NOV-23 8Q2E 0 JRNL AUTH L.MAZZEI,A.PAUL,M.CIANCI,M.DEVODIER,D.MANDELLI,P.CARLONI, JRNL AUTH 2 S.CIURLI JRNL TITL KINETIC AND STRUCTURAL DETAILS OF UREASE INACTIVATION BY JRNL TITL 2 THIURAM DISULPHIDES. JRNL REF J.INORG.BIOCHEM. V. 250 12398 2023 JRNL REFN ISSN 0162-0134 JRNL PMID 37879152 JRNL DOI 10.1016/J.JINORGBIO.2023.112398 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 114.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 104151 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5465 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) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7556 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 424 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6047 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 173 REMARK 3 SOLVENT ATOMS : 554 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -3.37000 REMARK 3 B12 (A**2) : 0.52000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.831 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6609 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 6320 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8941 ; 1.698 ; 1.662 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14613 ; 0.571 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 859 ; 6.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ; 8.377 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1148 ;13.967 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 996 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7816 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1392 ; 0.002 ; 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): 3312 ; 2.042 ; 2.532 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3311 ; 2.040 ; 2.531 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4181 ; 2.667 ; 4.536 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4182 ; 2.667 ; 4.538 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3297 ; 3.933 ; 3.034 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3234 ; 3.441 ; 2.926 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4654 ; 4.952 ; 5.186 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7365 ; 8.273 ;31.320 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7364 ; 8.273 ;31.320 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 : 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8Q2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-18 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 109674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 114.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.70 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.40 REMARK 200 R MERGE FOR SHELL (I) : 2.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RICE-SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CITRATE, PH 6.3, 1.6-2.1 M REMARK 280 AMMONIUM SULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 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,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 94.50850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 94.50850 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 94.50850 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 94.50850 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 94.50850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 94.50850 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: NONAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: NONAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 67840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 61180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -682.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 65.75550 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 113.89187 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -65.75550 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 113.89187 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 S SO4 C2321 LIES ON A SPECIAL POSITION. REMARK 375 S SO4 C2322 LIES ON A SPECIAL POSITION. REMARK 375 O1 SO4 C2322 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2514 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2694 LIES ON A SPECIAL POSITION. 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 OE1 GLU B 111 O HOH B 301 2.05 REMARK 500 O OH C 2316 O HOH C 2401 2.13 REMARK 500 O OH C 2316 O HOH C 2402 2.19 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 CYS C 520 CB - CA - C ANGL. DEV. = -20.2 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 ASN A 97 62.21 37.16 REMARK 500 ASN B 52 129.69 -29.92 REMARK 500 ILE B 99 -100.75 62.15 REMARK 500 ALA C 23 -133.19 54.18 REMARK 500 MET C 54 -115.61 -118.06 REMARK 500 HIS C 275 63.49 28.04 REMARK 500 HIS C 283 115.85 -30.32 REMARK 500 ASP C 363 35.81 71.94 REMARK 500 MET C 367 56.76 -160.40 REMARK 500 MET C 367 56.76 -160.40 REMARK 500 THR C 411 -84.47 -114.43 REMARK 500 VAL C 445 -64.51 -109.02 REMARK 500 ASN C 531 53.35 -146.17 REMARK 500 ALA C 564 -110.04 -137.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG C 234 0.09 SIDE CHAIN REMARK 500 ARG C 402 0.08 SIDE CHAIN REMARK 500 ARG C 513 0.12 SIDE CHAIN REMARK 500 ARG C 566 0.08 SIDE CHAIN 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 NI C2315 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 137 NE2 REMARK 620 2 HIS C 139 NE2 111.3 REMARK 620 3 KCX C 220 OQ2 94.3 91.8 REMARK 620 4 ASP C 363 OD1 80.8 85.4 173.1 REMARK 620 5 OH C2316 O 95.1 152.9 92.2 93.2 REMARK 620 6 HOH C2402 O 160.0 88.1 89.8 96.5 65.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C2314 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX C 220 OQ1 REMARK 620 2 HIS C 249 ND1 103.8 REMARK 620 3 HIS C 275 NE2 103.4 96.6 REMARK 620 4 OH C2316 O 92.1 152.9 100.9 REMARK 620 5 HOH C2401 O 106.8 90.8 146.2 63.4 REMARK 620 N 1 2 3 4 DBREF 8Q2E A 1 100 UNP P41022 URE3_SPOPA 1 100 DBREF 8Q2E B 5 126 UNP P41021 URE2_SPOPA 5 126 DBREF 8Q2E C 1 570 UNP P41020 URE1_SPOPA 1 570 SEQADV 8Q2E ALA A 20 UNP P41022 LEU 20 VARIANT SEQADV 8Q2E LYS A 22 UNP P41022 ARG 22 VARIANT SEQADV 8Q2E TYR C 35 UNP P41020 INSERTION SEQADV 8Q2E C UNP P41020 VAL 42 DELETION SEQRES 1 A 100 CXM HIS LEU ASN PRO ALA GLU LYS GLU LYS LEU GLN ILE SEQRES 2 A 100 PHE LEU ALA SER GLU LEU ALA LEU LYS ARG LYS ALA ARG SEQRES 3 A 100 GLY LEU LYS LEU ASN TYR PRO GLU ALA VAL ALA ILE ILE SEQRES 4 A 100 THR SER PHE ILE MET GLU GLY ALA ARG ASP GLY LYS THR SEQRES 5 A 100 VAL ALA MET LEU MET GLU GLU GLY LYS HIS VAL LEU THR SEQRES 6 A 100 ARG ASP ASP VAL MET GLU GLY VAL PRO GLU MET ILE ASP SEQRES 7 A 100 ASP ILE GLN ALA GLU ALA THR PHE PRO ASP GLY THR LYS SEQRES 8 A 100 LEU VAL THR VAL HIS ASN PRO ILE SER SEQRES 1 B 122 ASN TYR ILE VAL PRO GLY GLU TYR ARG VAL ALA GLU GLY SEQRES 2 B 122 GLU ILE GLU ILE ASN ALA GLY ARG GLU LYS THR THR ILE SEQRES 3 B 122 ARG VAL SER ASN THR GLY ASP ARG PRO ILE GLN VAL GLY SEQRES 4 B 122 SER HIS ILE HIS PHE VAL GLU VAL ASN LYS GLU LEU LEU SEQRES 5 B 122 PHE ASP ARG ALA GLU GLY ILE GLY ARG ARG LEU ASN ILE SEQRES 6 B 122 PRO SER GLY THR ALA ALA ARG PHE GLU PRO GLY GLU GLU SEQRES 7 B 122 MET GLU VAL GLU LEU THR GLU LEU GLY GLY ASN ARG GLU SEQRES 8 B 122 VAL PHE GLY ILE SER ASP LEU THR ASN GLY SER VAL ASP SEQRES 9 B 122 ASN LYS GLU LEU ILE LEU GLN ARG ALA LYS GLU LEU GLY SEQRES 10 B 122 TYR LYS GLY VAL GLU SEQRES 1 C 570 MET LYS ILE ASN ARG GLN GLN TYR ALA GLU SER TYR GLY SEQRES 2 C 570 PRO THR VAL GLY ASP GLN VAL ARG LEU ALA ASP THR ASP SEQRES 3 C 570 LEU TRP ILE GLU VAL GLU LYS ASP TYR THR THR TYR GLY SEQRES 4 C 570 ASP GLU ALA ASN PHE GLY GLY GLY LYS VAL LEU ARG GLU SEQRES 5 C 570 GLY MET GLY GLU ASN GLY THR TYR THR ARG THR GLU ASN SEQRES 6 C 570 VAL LEU ASP LEU LEU LEU THR ASN ALA LEU ILE LEU ASP SEQRES 7 C 570 TYR THR GLY ILE TYR LYS ALA ASP ILE GLY VAL LYS ASP SEQRES 8 C 570 GLY TYR ILE VAL GLY ILE GLY LYS GLY GLY ASN PRO ASP SEQRES 9 C 570 ILE MET ASP GLY VAL THR PRO ASN MET ILE VAL GLY THR SEQRES 10 C 570 ALA THR GLU VAL ILE ALA ALA GLU GLY LYS ILE VAL THR SEQRES 11 C 570 ALA GLY GLY ILE ASP THR HIS VAL HIS PHE ILE ASN PRO SEQRES 12 C 570 ASP GLN VAL ASP VAL ALA LEU ALA ASN GLY ILE THR THR SEQRES 13 C 570 LEU PHE GLY GLY GLY THR GLY PRO ALA GLU GLY SER LYS SEQRES 14 C 570 ALA THR THR VAL THR PRO GLY PRO TRP ASN ILE GLU LYS SEQRES 15 C 570 MET LEU LYS SER THR GLU GLY LEU PRO ILE ASN VAL GLY SEQRES 16 C 570 ILE LEU GLY LYS GLY HIS GLY SER SER ILE ALA PRO ILE SEQRES 17 C 570 MET GLU GLN ILE ASP ALA GLY ALA ALA GLY LEU KCX ILE SEQRES 18 C 570 HIS GLU ASP TRP GLY ALA THR PRO ALA SER ILE ASP ARG SEQRES 19 C 570 SER LEU THR VAL ALA ASP GLU ALA ASP VAL GLN VAL ALA SEQRES 20 C 570 ILE HIS SER ASP THR LEU ASN GLU ALA GLY PHE LEU GLU SEQRES 21 C 570 ASP THR LEU ARG ALA ILE ASN GLY ARG VAL ILE HIS SER SEQRES 22 C 570 PHE HIS VAL GLU GLY ALA GLY GLY GLY HIS ALA PRO ASP SEQRES 23 C 570 ILE MET ALA MET ALA GLY HIS PRO ASN VAL LEU PRO SER SEQRES 24 C 570 SER THR ASN PRO THR ARG PRO PHE THR VAL ASN THR ILE SEQRES 25 C 570 ASP GLU HIS LEU ASP MET LEU MET VAL CYS HIS HIS LEU SEQRES 26 C 570 LYS GLN ASN ILE PRO GLU ASP VAL ALA PHE ALA ASP SER SEQRES 27 C 570 ARG ILE ARG PRO GLU THR ILE ALA ALA GLU ASP ILE LEU SEQRES 28 C 570 HIS ASP LEU GLY ILE ILE SER MET MET SER THR ASP ALA SEQRES 29 C 570 LEU ALA MET GLY ARG ALA GLY GLU MET VAL LEU ARG THR SEQRES 30 C 570 TRP GLN THR ALA ASP LYS MET LYS LYS GLN ARG GLY PRO SEQRES 31 C 570 LEU ALA GLU GLU LYS ASN GLY SER ASP ASN PHE ARG ALA SEQRES 32 C 570 LYS ARG TYR VAL SER LYS TYR THR ILE ASN PRO ALA ILE SEQRES 33 C 570 ALA GLN GLY ILE ALA HIS GLU VAL GLY SER ILE GLU GLU SEQRES 34 C 570 GLY LYS PHE ALA ASP LEU VAL LEU TRP GLU PRO LYS PHE SEQRES 35 C 570 PHE GLY VAL LYS ALA ASP ARG VAL ILE LYS GLY GLY ILE SEQRES 36 C 570 ILE ALA TYR ALA GLN ILE GLY ASP PRO SER ALA SER ILE SEQRES 37 C 570 PRO THR PRO GLN PRO VAL MET GLY ARG ARG MET TYR GLY SEQRES 38 C 570 THR VAL GLY ASP LEU ILE HIS ASP THR ASN ILE THR PHE SEQRES 39 C 570 MET SER LYS SER SER ILE GLN GLN GLY VAL PRO ALA LYS SEQRES 40 C 570 LEU GLY LEU LYS ARG ARG ILE GLY THR VAL LYS ASN CYS SEQRES 41 C 570 ARG ASN ILE GLY LYS LYS ASP MET LYS TRP ASN ASP VAL SEQRES 42 C 570 THR THR ASP ILE ASP ILE ASN PRO GLU THR TYR GLU VAL SEQRES 43 C 570 LYS VAL ASP GLY GLU VAL LEU THR CYS GLU PRO VAL LYS SEQRES 44 C 570 GLU LEU PRO MET ALA GLN ARG TYR PHE LEU PHE MODRES 8Q2E CXM A 1 MET MODIFIED RESIDUE MODRES 8Q2E KCX C 220 LYS MODIFIED RESIDUE HET CXM A 1 11 HET KCX C 220 12 HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET SO4 A 207 5 HET SO4 A 208 5 HET SO4 A 209 5 HET SO4 A 210 5 HET EDO B 201 4 HET EDO B 202 4 HET EDO B 203 4 HET SO4 B 204 5 HET SO4 B 205 5 HET SO4 B 206 5 HET SO4 B 207 5 HET SO4 B 208 5 HET EDO C2301 4 HET EDO C2302 4 HET EDO C2303 4 HET EDO C2304 4 HET EDO C2305 4 HET EDO C2306 4 HET EDO C2307 4 HET EDO C2308 4 HET EDO C2309 4 HET EDO C2310 4 HET EDO C2311 4 HET EDO C2312 4 HET IS9 C2313 6 HET NI C2314 1 HET NI C2315 1 HET OH C2316 1 HET SO4 C2317 5 HET SO4 C2318 5 HET SO4 C2319 5 HET SO4 C2320 5 HET SO4 C2321 5 HET SO4 C2322 5 HET SO4 C2323 5 HETNAM CXM N-CARBOXYMETHIONINE HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM IS9 DIMETHYLCARBAMODITHIOIC ACID HETNAM NI NICKEL (II) ION HETNAM OH HYDROXIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CXM C6 H11 N O4 S FORMUL 3 KCX C7 H14 N2 O4 FORMUL 4 EDO 21(C2 H6 O2) FORMUL 10 SO4 16(O4 S 2-) FORMUL 34 IS9 C3 H7 N S2 FORMUL 35 NI 2(NI 2+) FORMUL 37 OH H O 1- FORMUL 45 HOH *554(H2 O) HELIX 1 AA1 ASN A 4 ARG A 26 1 23 HELIX 2 AA2 ASN A 31 ASP A 49 1 19 HELIX 3 AA3 THR A 52 GLY A 60 1 9 HELIX 4 AA4 LYS A 61 VAL A 63 5 3 HELIX 5 AA5 THR A 65 VAL A 69 5 5 HELIX 6 AA6 GLY A 72 ILE A 77 1 6 HELIX 7 AA7 HIS B 47 VAL B 51 5 5 HELIX 8 AA8 ASP B 58 ILE B 63 5 6 HELIX 9 AA9 ASN B 109 GLY B 121 1 13 HELIX 10 AB1 ARG C 5 GLY C 13 1 9 HELIX 11 AB2 ASP C 144 ASN C 152 1 9 HELIX 12 AB3 ALA C 165 THR C 171 1 7 HELIX 13 AB4 PRO C 175 GLU C 188 1 14 HELIX 14 AB5 SER C 204 GLY C 215 1 12 HELIX 15 AB6 ASP C 224 GLY C 226 5 3 HELIX 16 AB7 THR C 228 ASP C 243 1 16 HELIX 17 AB8 PHE C 258 ASN C 267 1 10 HELIX 18 AB9 ASP C 286 HIS C 293 5 8 HELIX 19 AC1 ASN C 310 HIS C 323 1 14 HELIX 20 AC2 ILE C 329 ILE C 340 1 12 HELIX 21 AC3 ARG C 341 LEU C 354 1 14 HELIX 22 AC4 GLU C 372 GLY C 389 1 18 HELIX 23 AC5 ASP C 399 THR C 411 1 13 HELIX 24 AC6 THR C 411 GLY C 419 1 9 HELIX 25 AC7 GLU C 439 PHE C 443 5 5 HELIX 26 AC8 TYR C 480 GLY C 484 5 5 HELIX 27 AC9 ASP C 485 THR C 490 1 6 HELIX 28 AD1 SER C 496 GLN C 502 1 7 HELIX 29 AD2 GLY C 503 GLY C 509 1 7 HELIX 30 AD3 GLY C 524 MET C 528 5 5 SHEET 1 AA1 2 ASP A 79 PHE A 86 0 SHEET 2 AA1 2 GLY A 89 HIS A 96 -1 O VAL A 95 N ILE A 80 SHEET 1 AA2 3 TYR B 12 ARG B 13 0 SHEET 2 AA2 3 GLN C 19 ARG C 21 -1 O GLN C 19 N ARG B 13 SHEET 3 AA2 3 TRP C 28 GLU C 30 -1 O ILE C 29 N VAL C 20 SHEET 1 AA3 2 GLU B 18 GLU B 20 0 SHEET 2 AA3 2 LYS C 2 ASN C 4 -1 O ILE C 3 N ILE B 19 SHEET 1 AA4 4 LEU B 55 LEU B 56 0 SHEET 2 AA4 4 LYS B 27 ASN B 34 -1 N SER B 33 O LEU B 56 SHEET 3 AA4 4 GLU B 82 GLU B 89 -1 O LEU B 87 N THR B 28 SHEET 4 AA4 4 ARG B 65 LEU B 67 -1 N ARG B 66 O THR B 88 SHEET 1 AA5 2 ILE B 40 GLY B 43 0 SHEET 2 AA5 2 ALA B 74 PHE B 77 -1 O PHE B 77 N ILE B 40 SHEET 1 AA6 2 GLU B 95 VAL B 96 0 SHEET 2 AA6 2 GLY B 105 SER B 106 -1 O GLY B 105 N VAL B 96 SHEET 1 AA7 4 TYR C 93 GLY C 98 0 SHEET 2 AA7 4 GLY C 81 LYS C 90 -1 N GLY C 88 O GLY C 96 SHEET 3 AA7 4 LEU C 69 ASP C 78 -1 N ILE C 76 O TYR C 83 SHEET 4 AA7 4 GLU C 120 ALA C 123 1 O ILE C 122 N THR C 72 SHEET 1 AA8 8 TYR C 93 GLY C 98 0 SHEET 2 AA8 8 GLY C 81 LYS C 90 -1 N GLY C 88 O GLY C 96 SHEET 3 AA8 8 LEU C 69 ASP C 78 -1 N ILE C 76 O TYR C 83 SHEET 4 AA8 8 ILE C 128 ALA C 131 1 O VAL C 129 N LEU C 75 SHEET 5 AA8 8 LEU C 435 TRP C 438 -1 O VAL C 436 N THR C 130 SHEET 6 AA8 8 ARG C 449 LYS C 452 -1 O ILE C 451 N LEU C 435 SHEET 7 AA8 8 ILE C 455 ILE C 461 -1 O TYR C 458 N VAL C 450 SHEET 8 AA8 8 MET C 475 ARG C 478 -1 O ARG C 477 N ALA C 459 SHEET 1 AA9 7 GLY C 133 HIS C 139 0 SHEET 2 AA9 7 ILE C 154 GLY C 160 1 O PHE C 158 N ASP C 135 SHEET 3 AA9 7 ASN C 193 LYS C 199 1 O ASN C 193 N LEU C 157 SHEET 4 AA9 7 GLY C 218 HIS C 222 1 O GLY C 218 N GLY C 198 SHEET 5 AA9 7 GLN C 245 HIS C 249 1 O ALA C 247 N ILE C 221 SHEET 6 AA9 7 ILE C 271 SER C 273 1 O HIS C 272 N VAL C 246 SHEET 7 AA9 7 VAL C 296 PRO C 298 1 O LEU C 297 N ILE C 271 SHEET 1 AB1 5 GLY C 133 HIS C 139 0 SHEET 2 AB1 5 ILE C 154 GLY C 160 1 O PHE C 158 N ASP C 135 SHEET 3 AB1 5 ASN C 193 LYS C 199 1 O ASN C 193 N LEU C 157 SHEET 4 AB1 5 ILE C 492 MET C 495 1 O PHE C 494 N VAL C 194 SHEET 5 AB1 5 ARG C 513 THR C 516 1 O ARG C 513 N THR C 493 SHEET 1 AB2 3 ILE C 537 ILE C 539 0 SHEET 2 AB2 3 VAL C 546 VAL C 548 -1 O LYS C 547 N ASP C 538 SHEET 3 AB2 3 GLU C 551 VAL C 552 -1 O GLU C 551 N VAL C 548 LINK C CXM A 1 N HIS A 2 1555 1555 1.37 LINK C LEU C 219 N KCX C 220 1555 1555 1.33 LINK C KCX C 220 N ILE C 221 1555 1555 1.36 LINK SG CYS C 322 S IS9 C2313 1555 1555 2.12 LINK NE2 HIS C 137 NI NI C2315 1555 1555 2.07 LINK NE2 HIS C 139 NI NI C2315 1555 1555 2.09 LINK OQ1 KCX C 220 NI NI C2314 1555 1555 1.99 LINK OQ2 KCX C 220 NI NI C2315 1555 1555 2.02 LINK ND1 HIS C 249 NI NI C2314 1555 1555 1.99 LINK NE2 HIS C 275 NI NI C2314 1555 1555 2.00 LINK OD1 ASP C 363 NI NI C2315 1555 1555 2.05 LINK NI NI C2314 O OH C2316 1555 1555 2.02 LINK NI NI C2314 O HOH C2401 1555 1555 2.04 LINK NI NI C2315 O OH C2316 1555 1555 2.03 LINK NI NI C2315 O HOH C2402 1555 1555 2.04 CISPEP 1 ALA C 284 PRO C 285 0 -0.35 CISPEP 2 ARG C 305 PRO C 306 0 -14.50 CISPEP 3 GLN C 472 PRO C 473 0 -0.31 CRYST1 131.511 131.511 189.017 90.00 90.00 120.00 P 63 2 2 12 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 0.007604 0.004390 0.000000 0.00000 SCALE2 0.000000 0.008780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005291 0.00000 HETATM 1 N CXM A 1 -15.592 72.294 88.232 1.00 26.28 N HETATM 2 CA CXM A 1 -15.273 73.632 88.710 1.00 25.56 C HETATM 3 CB CXM A 1 -13.769 73.777 89.041 1.00 26.68 C HETATM 4 CG CXM A 1 -13.330 73.074 90.360 1.00 28.03 C HETATM 5 SD CXM A 1 -11.570 73.344 90.673 1.00 30.28 S HETATM 6 CE CXM A 1 -10.869 72.252 89.448 1.00 36.00 C HETATM 7 C CXM A 1 -15.618 74.699 87.659 1.00 24.86 C HETATM 8 O CXM A 1 -15.973 75.863 88.010 1.00 23.87 O HETATM 9 CN CXM A 1 -16.859 72.020 87.785 1.00 32.05 C HETATM 10 ON1 CXM A 1 -17.047 70.744 87.464 1.00 28.16 O HETATM 11 ON2 CXM A 1 -17.767 72.814 87.709 1.00 30.24 O