HEADER HYDROLASE 29-MAR-22 7ZCY TITLE SPOROSARCINA PASTEURII UREASE (SPU) CO-CRYSTALLIZED IN THE PRESENCE OF TITLE 2 AN EBSELEN-DERIVATIVE AND BOUND TO SE ATOMS 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 ATCC: 11859; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 7 ORGANISM_TAXID: 1474; SOURCE 8 ATCC: 11859; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 11 ORGANISM_TAXID: 1474; SOURCE 12 ATCC: 11859 KEYWDS UREASE, NICKEL, EBSELEN, SELENIUM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MAZZEI,S.CIURLI,M.CIANCI REVDAT 5 07-FEB-24 7ZCY 1 REMARK REVDAT 4 15-NOV-23 7ZCY 1 REMARK REVDAT 3 08-NOV-23 7ZCY 1 JRNL REVDAT 2 01-NOV-23 7ZCY 1 JRNL REVDAT 1 19-APR-23 7ZCY 0 JRNL AUTH K.MACEGONIUK,W.TABOR,L.MAZZEI,M.CIANCI,M.GIURG,K.OLECH, JRNL AUTH 2 M.BURDA-GRABOWSKA,R.KALETA,A.GRABOWIECKA,A.MUCHA,S.CIURLI, JRNL AUTH 3 L.BERLICKI JRNL TITL OPTIMIZED EBSELEN-BASED INHIBITORS OF BACTERIAL UREASES WITH JRNL TITL 2 NONTYPICAL MODE OF ACTION. JRNL REF J.MED.CHEM. V. 66 2054 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 36661843 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01799 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 134952 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) : 0.137 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7016 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9864 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 512 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 143 REMARK 3 SOLVENT ATOMS : 767 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -2.26000 REMARK 3 B12 (A**2) : 0.35000 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): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.359 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.980 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6640 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6355 ; 0.003 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8976 ; 1.806 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14692 ; 1.500 ; 1.585 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 864 ; 7.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 333 ;33.735 ;22.793 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1149 ;12.928 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.263 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 871 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7718 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1418 ; 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): 3340 ; 1.844 ; 2.392 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3339 ; 1.842 ; 2.392 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4222 ; 2.530 ; 3.580 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4223 ; 2.530 ; 3.581 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3299 ; 3.237 ; 2.789 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3299 ; 3.234 ; 2.788 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4744 ; 4.506 ; 4.036 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7461 ; 5.922 ;30.361 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7462 ; 5.923 ;30.370 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 7ZCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3-6.7 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) : 0.9763 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 : 142031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 189.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.50 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.90 REMARK 200 R MERGE FOR SHELL (I) : 2.30100 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: 5G4H REMARK 200 REMARK 200 REMARK: RICE SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN-LIGAND (1 MM LIGAND REMARK 280 CONCENTRATION) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO REMARK 280 CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH 1.6-2.1 M AMMONIUM REMARK 280 SULFATE ALSO CONTAINING 100 MM SODIUM CITRATE AT PH 6.3, COUNTER- REMARK 280 DIFFUSION, 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 94.50150 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 94.50150 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 94.50150 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 94.50150 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 94.50150 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 94.50150 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: 65660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -446.0 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 65.80600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 113.97934 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -65.80600 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 113.97934 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 C 608 LIES ON A SPECIAL POSITION. REMARK 375 O4 SO4 C 608 LIES ON A SPECIAL POSITION. REMARK 375 S SO4 C 609 LIES ON A SPECIAL POSITION. REMARK 375 HOH C1013 LIES ON A SPECIAL POSITION. REMARK 375 HOH C1026 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 O HOH C 930 O HOH C 1140 2.19 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 B 52 133.40 -31.32 REMARK 500 ASN B 52 120.71 -31.32 REMARK 500 LYS B 53 -38.34 -38.08 REMARK 500 ILE B 99 -99.12 59.01 REMARK 500 ALA C 23 -134.49 51.95 REMARK 500 MET C 54 -119.66 -118.34 REMARK 500 PRO C 103 0.19 -65.04 REMARK 500 HIS C 275 63.46 27.98 REMARK 500 HIS C 283 116.86 -31.51 REMARK 500 ASP C 363 35.86 72.48 REMARK 500 MET C 367 57.93 -162.44 REMARK 500 MET C 367 57.93 -160.23 REMARK 500 THR C 411 -84.87 -116.99 REMARK 500 VAL C 445 -62.84 -106.24 REMARK 500 ASN C 522 50.20 -117.66 REMARK 500 ASN C 531 56.04 -147.05 REMARK 500 ASP C 549 65.21 35.28 REMARK 500 ALA C 564 -112.55 -138.59 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 C 602 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 137 NE2 REMARK 620 2 HIS C 139 NE2 109.3 REMARK 620 3 KCX C 220 OQ1 93.9 91.4 REMARK 620 4 ASP C 363 OD1 81.8 86.2 174.0 REMARK 620 5 OH C 603 O 95.9 153.7 94.1 90.5 REMARK 620 6 HOH C 703 O 160.1 89.7 91.3 94.2 64.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 601 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX C 220 OQ2 REMARK 620 2 HIS C 249 ND1 101.8 REMARK 620 3 HIS C 275 NE2 105.0 97.3 REMARK 620 4 OH C 603 O 94.1 153.3 99.3 REMARK 620 5 HOH C 702 O 107.8 91.1 143.7 63.3 REMARK 620 N 1 2 3 4 DBREF 7ZCY A 1 100 UNP P41022 URE3_SPOPA 1 100 DBREF 7ZCY B 5 126 UNP P41021 URE2_SPOPA 5 126 DBREF 7ZCY C 1 570 UNP P41020 URE1_SPOPA 1 570 SEQADV 7ZCY ALA A 20 UNP P41022 LEU 20 VARIANT SEQADV 7ZCY LYS A 22 UNP P41022 ARG 22 VARIANT SEQADV 7ZCY TYR C 35 UNP P41020 INSERTION SEQADV 7ZCY 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 7ZCY CXM A 1 MET MODIFIED RESIDUE MODRES 7ZCY KCX C 220 LYS MODIFIED RESIDUE HET CXM A 1 22 HET KCX C 220 12 HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HET SO4 A 204 5 HET EDO A 205 4 HET EDO A 206 4 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 B 203 5 HET NI C 601 1 HET NI C 602 1 HET OH C 603 1 HET EDO C 604 4 HET IU9 C 605 18 HET SO4 C 606 5 HET SO4 C 607 5 HET SO4 C 608 5 HET SO4 C 609 5 HET EDO C 610 4 HET EDO C 611 4 HET EDO C 612 4 HET EDO C 613 4 HET EDO C 614 4 HET EDO C 615 4 HET EDO C 616 4 HET EDO C 617 4 HET EDO C 618 4 HET EDO C 619 4 HET EDO C 620 4 HET EDO C 621 4 HET EDO C 622 4 HET EDO C 623 4 HET SE C 624 1 HET SE C 625 1 HETNAM CXM N-CARBOXYMETHIONINE HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM OH HYDROXIDE ION HETNAM IU9 N-(2-CHLORANYL-4-FLUORANYL-PHENYL)-2-SELANYL-BENZAMIDE HETNAM SE SELENIUM ATOM HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CXM C6 H11 N O4 S FORMUL 3 KCX C7 H14 N2 O4 FORMUL 4 EDO 20(C2 H6 O2) FORMUL 7 SO4 8(O4 S 2-) FORMUL 13 NI 2(NI 2+) FORMUL 15 OH H O 1- FORMUL 17 IU9 C13 H9 CL F N O SE FORMUL 36 SE 2(SE) FORMUL 38 HOH *767(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 LYS C 409 1 11 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 LYS C 497 GLN C 502 1 6 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 LEU C 70 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 ALA C 457 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 SER C 496 1 O PHE C 494 N VAL C 194 SHEET 5 AB1 5 ARG C 513 VAL C 517 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 ACXM A 1 N HIS A 2 1555 1555 1.34 LINK C BCXM A 1 N HIS A 2 1555 1555 1.34 LINK C LEU C 219 N KCX C 220 1555 1555 1.33 LINK C KCX C 220 N ILE C 221 1555 1555 1.35 LINK SG CYS C 322 SE SE C 624 1555 1555 2.25 LINK SG CYS C 555 SE IU9 C 605 1555 1555 2.42 LINK SE SE C 624 SE SE C 625 1555 1555 2.35 LINK NE2 HIS C 137 NI NI C 602 1555 1555 2.08 LINK NE2 HIS C 139 NI NI C 602 1555 1555 2.05 LINK OQ2 KCX C 220 NI NI C 601 1555 1555 1.97 LINK OQ1 KCX C 220 NI NI C 602 1555 1555 2.08 LINK ND1 HIS C 249 NI NI C 601 1555 1555 2.01 LINK NE2 HIS C 275 NI NI C 601 1555 1555 1.99 LINK OD1 ASP C 363 NI NI C 602 1555 1555 2.13 LINK NI NI C 601 O OH C 603 1555 1555 2.08 LINK NI NI C 601 O HOH C 702 1555 1555 2.11 LINK NI NI C 602 O OH C 603 1555 1555 2.08 LINK NI NI C 602 O HOH C 703 1555 1555 2.10 CISPEP 1 ALA C 284 PRO C 285 0 0.01 CISPEP 2 ARG C 305 PRO C 306 0 -16.59 CISPEP 3 GLN C 472 PRO C 473 0 1.70 CRYST1 131.612 131.612 189.003 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 0.007598 0.004387 0.000000 0.00000 SCALE2 0.000000 0.008774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005291 0.00000 HETATM 1 N ACXM A 1 -15.595 72.299 88.094 0.80 22.99 N HETATM 2 N BCXM A 1 -15.555 72.397 88.351 0.20 22.63 N HETATM 3 CA ACXM A 1 -15.292 73.617 88.653 0.80 22.69 C HETATM 4 CA BCXM A 1 -15.243 73.766 88.729 0.20 21.64 C HETATM 5 CB ACXM A 1 -13.799 73.772 89.010 0.80 25.95 C HETATM 6 CB BCXM A 1 -13.758 73.912 89.098 0.20 21.47 C HETATM 7 CG ACXM A 1 -13.368 73.023 90.273 0.80 26.32 C HETATM 8 CG BCXM A 1 -13.405 73.201 90.400 0.20 20.74 C HETATM 9 SD ACXM A 1 -11.641 73.395 90.651 0.80 29.66 S HETATM 10 SD BCXM A 1 -11.625 73.107 90.697 0.20 20.34 S HETATM 11 CE ACXM A 1 -10.842 72.329 89.450 0.80 26.89 C HETATM 12 CE BCXM A 1 -11.273 74.818 91.097 0.20 19.10 C HETATM 13 C ACXM A 1 -15.623 74.734 87.655 0.80 23.67 C HETATM 14 C BCXM A 1 -15.636 74.772 87.643 0.20 21.97 C HETATM 15 O ACXM A 1 -15.918 75.874 88.039 0.80 23.19 O HETATM 16 O BCXM A 1 -16.091 75.871 87.960 0.20 22.02 O HETATM 17 CN ACXM A 1 -16.857 71.996 87.682 0.80 24.92 C HETATM 18 CN BCXM A 1 -16.817 72.059 88.019 0.20 23.78 C HETATM 19 ON1ACXM A 1 -17.051 70.777 87.313 0.80 23.09 O HETATM 20 ON1BCXM A 1 -17.063 70.756 87.975 0.20 23.80 O HETATM 21 ON2ACXM A 1 -17.793 72.781 87.658 0.80 27.23 O HETATM 22 ON2BCXM A 1 -17.686 72.874 87.805 0.20 24.47 O