PDB Short entry for 4B5G HEADER HYDROLASE/DNA 03-AUG-12 4B5G TITLE SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS TITLE 2 (CRYSTAL FORM 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXODEOXYRIBONUCLEASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NEISSERIA AP ENDONUCLEASE; COMPND 5 EC: 3.1.11.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'; COMPND 9 CHAIN: U, W, Y; COMPND 10 SYNONYM: DNA 11MER CONTAINING ABASIC RESIDUE; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'; COMPND 14 CHAIN: V, X, Z; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 9 ORGANISM_TAXID: 487; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 13 ORGANISM_TAXID: 487 KEYWDS HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.LU,J.SILHAN,J.T.MACDONALD,E.P.CARPENTER,K.JENSEN,C.M.TANG, AUTHOR 2 G.S.BALDWIN,P.S.FREEMONT REVDAT 3 28-FEB-18 4B5G 1 JRNL REVDAT 2 31-OCT-12 4B5G 1 JRNL REVDAT 1 17-OCT-12 4B5G 0 JRNL AUTH D.LU,J.SILHAN,J.T.MACDONALD,E.P.CARPENTER,K.JENSEN,C.M.TANG, JRNL AUTH 2 G.S.BALDWIN,P.S.FREEMONT JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE OF ABASIC JRNL TITL 2 DNA IN NEISSERIA MENINGITIDIS. JRNL REF PROC. NATL. ACAD. SCI. V. 109 16852 2012 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 23035246 JRNL DOI 10.1073/PNAS.1206563109 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1084) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 27545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1404 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 44.0812 - 5.9206 0.98 3032 168 0.2232 0.2231 REMARK 3 2 5.9206 - 4.7011 1.00 2891 139 0.1916 0.2304 REMARK 3 3 4.7011 - 4.1073 0.99 2806 166 0.1922 0.2096 REMARK 3 4 4.1073 - 3.7320 0.98 2744 159 0.2348 0.2952 REMARK 3 5 3.7320 - 3.4646 0.96 2723 130 0.2532 0.2681 REMARK 3 6 3.4646 - 3.2604 0.95 2611 147 0.2568 0.3269 REMARK 3 7 3.2604 - 3.0972 0.94 2636 134 0.2772 0.3232 REMARK 3 8 3.0972 - 2.9624 0.92 2552 129 0.3063 0.3116 REMARK 3 9 2.9624 - 2.8484 0.81 2218 120 0.3380 0.3780 REMARK 3 10 2.8484 - 2.7501 0.70 1928 112 0.3927 0.4039 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 7908 REMARK 3 ANGLE : 0.808 10959 REMARK 3 CHIRALITY : 0.052 1122 REMARK 3 PLANARITY : 0.002 1191 REMARK 3 DIHEDRAL : 19.131 2988 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 4B5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053621. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : NULL 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 75.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 190.34150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.62050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.62050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.17075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.62050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.62050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 285.51225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.62050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.62050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.17075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.62050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.62050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 285.51225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 190.34150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U, V 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, W, X 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, Y, Z 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 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 GLU A 259 O REMARK 470 GLU B 259 O REMARK 470 GLU C 259 O 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 VAL A 9 O HOH A 2001 2.12 REMARK 500 O ILE B 152 OH TYR B 222 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 DG X 51 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT Y 33 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA Y 34 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC Y 35 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT Z 45 O4' - C1' - N1 ANGL. DEV. = 1.9 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 GLU A 36 61.62 60.48 REMARK 500 SER A 67 -146.35 52.97 REMARK 500 PHE A 100 54.06 -118.21 REMARK 500 PHE A 171 36.32 -142.19 REMARK 500 GLU B 36 60.37 61.20 REMARK 500 SER B 67 -147.42 51.59 REMARK 500 PHE B 100 54.43 -116.87 REMARK 500 ASN B 161 75.60 -104.32 REMARK 500 PHE B 171 35.25 -141.41 REMARK 500 SER C 67 -146.83 51.55 REMARK 500 PHE C 100 54.21 -118.79 REMARK 500 PHE C 171 36.41 -141.83 REMARK 500 ALA C 258 -27.94 -159.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B5F RELATED DB: PDB REMARK 900 SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS REMARK 900 (CRYSTAL FORM 1) REMARK 900 RELATED ID: 4B5H RELATED DB: PDB REMARK 900 SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN REMARK 900 PRESENCE OF METAL IONS REMARK 900 RELATED ID: 4B5I RELATED DB: PDB REMARK 900 PRODUCT COMPLEX OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL REMARK 900 IONS REMARK 900 RELATED ID: 4B5J RELATED DB: PDB REMARK 900 NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN REMARK 900 ADENINE BASE REMARK 900 RELATED ID: 4B5M RELATED DB: PDB REMARK 900 NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE REMARK 900 ORPHAN BASE DBREF 4B5G A 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5G B 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5G C 1 259 UNP C9X331 C9X331_NEIM8 1 259 DBREF 4B5G U 31 41 PDB 4B5G 4B5G 31 41 DBREF 4B5G V 42 52 PDB 4B5G 4B5G 42 52 DBREF 4B5G W 31 41 PDB 4B5G 4B5G 31 41 DBREF 4B5G X 42 52 PDB 4B5G 4B5G 42 52 DBREF 4B5G Y 31 41 PDB 4B5G 4B5G 31 41 DBREF 4B5G Z 42 52 PDB 4B5G 4B5G 42 52 SEQADV 4B5G GLY A 101 UNP C9X331 ASP 101 CONFLICT SEQADV 4B5G GLY B 101 UNP C9X331 ASP 101 CONFLICT SEQADV 4B5G GLY C 101 UNP C9X331 ASP 101 CONFLICT SEQRES 1 A 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 A 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 A 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 A 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 A 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 A 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 A 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 A 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 A 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 A 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 A 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 A 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 A 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 A 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 A 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 A 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 A 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 A 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 A 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 A 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 B 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 B 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 B 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 B 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 B 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 B 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 B 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 B 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 B 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 B 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 B 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 B 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 B 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 B 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 B 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 B 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 B 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 B 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 B 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 B 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 C 259 MET LEU LYS ILE ILE SER ALA ASN VAL ASN GLY ILE ARG SEQRES 2 C 259 SER ALA TYR LYS LYS GLY PHE TYR GLU TYR ILE ALA ALA SEQRES 3 C 259 SER GLY ALA ASP ILE VAL CYS VAL GLN GLU LEU LYS ALA SEQRES 4 C 259 GLN GLU ALA ASP LEU SER ALA ASP MET LYS ASN PRO HIS SEQRES 5 C 259 GLY MET HIS GLY HIS TRP HIS CYS ALA GLU LYS ARG GLY SEQRES 6 C 259 TYR SER GLY VAL ALA VAL TYR SER LYS ARG LYS PRO ASP SEQRES 7 C 259 ASN VAL GLN ILE GLY MET GLY ILE GLU GLU PHE ASP ARG SEQRES 8 C 259 GLU GLY ARG PHE VAL ARG CYS ASP PHE GLY ARG LEU SER SEQRES 9 C 259 VAL ILE SER LEU TYR LEU PRO SER GLY SER SER ALA GLU SEQRES 10 C 259 GLU ARG GLN GLN VAL LYS TYR ARG PHE LEU ASP ALA PHE SEQRES 11 C 259 TYR PRO MET LEU GLU ALA MET LYS ASN GLU GLY ARG ASP SEQRES 12 C 259 ILE VAL VAL CYS GLY ASP TRP ASN ILE ALA HIS GLN ASN SEQRES 13 C 259 ILE ASP LEU LYS ASN TRP LYS GLY ASN GLN LYS ASN SER SEQRES 14 C 259 GLY PHE LEU PRO GLU GLU ARG GLU TRP ILE GLY LYS VAL SEQRES 15 C 259 ILE HIS LYS LEU GLY TRP THR ASP MET TRP ARG THR LEU SEQRES 16 C 259 TYR PRO ASP VAL PRO GLY TYR THR TRP TRP SER ASN ARG SEQRES 17 C 259 GLY GLN ALA TYR ALA LYS ASP VAL GLY TRP ARG ILE ASP SEQRES 18 C 259 TYR GLN MET VAL THR PRO GLU LEU ALA ALA LYS ALA VAL SEQRES 19 C 259 SER ALA HIS VAL TYR LYS ASP GLU LYS PHE SER ASP HIS SEQRES 20 C 259 ALA PRO LEU VAL VAL GLU TYR ASP TYR ALA ALA GLU SEQRES 1 U 11 DG DC DT DA DC 3DR DC DA DT DC DG SEQRES 1 V 11 DC DG DA DT DG DG DG DT DA DG DC SEQRES 1 W 11 DG DC DT DA DC 3DR DC DA DT DC DG SEQRES 1 X 11 DC DG DA DT DG DG DG DT DA DG DC SEQRES 1 Y 11 DG DC DT DA DC 3DR DC DA DT DC DG SEQRES 1 Z 11 DC DG DA DT DG DG DG DT DA DG DC HET 3DR U 36 11 HET 3DR W 36 11 HET 3DR Y 36 11 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 4 3DR 3(C5 H11 O6 P) FORMUL 10 HOH *3(H2 O) HELIX 1 1 GLY A 11 LYS A 18 1 8 HELIX 2 2 GLY A 19 SER A 27 1 9 HELIX 3 3 ASN A 50 MET A 54 5 5 HELIX 4 4 ILE A 86 ARG A 91 1 6 HELIX 5 5 ALA A 116 ASN A 139 1 24 HELIX 6 6 GLN A 155 ASP A 158 5 4 HELIX 7 7 LEU A 172 LYS A 185 1 14 HELIX 8 8 MET A 191 TYR A 196 1 6 HELIX 9 9 THR A 226 ALA A 231 1 6 HELIX 10 10 GLY B 11 LYS B 18 1 8 HELIX 11 11 GLY B 19 SER B 27 1 9 HELIX 12 12 ASN B 50 MET B 54 5 5 HELIX 13 13 ILE B 86 ARG B 91 1 6 HELIX 14 14 ALA B 116 ASN B 139 1 24 HELIX 15 15 GLN B 155 ASP B 158 5 4 HELIX 16 16 LEU B 172 HIS B 184 1 13 HELIX 17 17 MET B 191 TYR B 196 1 6 HELIX 18 18 THR B 226 ALA B 231 1 6 HELIX 19 19 GLY C 11 LYS C 18 1 8 HELIX 20 20 GLY C 19 SER C 27 1 9 HELIX 21 21 ASN C 50 MET C 54 5 5 HELIX 22 22 ILE C 86 ARG C 91 1 6 HELIX 23 23 ALA C 116 ASN C 139 1 24 HELIX 24 24 GLN C 155 ASP C 158 5 4 HELIX 25 25 LEU C 172 LYS C 185 1 14 HELIX 26 26 MET C 191 TYR C 196 1 6 HELIX 27 27 THR C 226 ALA C 231 1 6 SHEET 1 AA 6 HIS A 55 HIS A 59 0 SHEET 2 AA 6 VAL A 69 SER A 73 -1 O VAL A 69 N HIS A 59 SHEET 3 AA 6 ILE A 31 GLN A 35 -1 O VAL A 32 N TYR A 72 SHEET 4 AA 6 LEU A 2 ASN A 8 1 O ILE A 5 N CYS A 33 SHEET 5 AA 6 LEU A 250 TYR A 254 -1 O LEU A 250 N SER A 6 SHEET 6 AA 6 ALA A 233 VAL A 238 -1 N VAL A 234 O GLU A 253 SHEET 1 AB 6 ASN A 79 ILE A 82 0 SHEET 2 AB 6 PHE A 95 PHE A 100 -1 O ARG A 97 N GLN A 81 SHEET 3 AB 6 LEU A 103 TYR A 109 -1 O LEU A 103 N PHE A 100 SHEET 4 AB 6 ASP A 143 ASP A 149 1 O ASP A 143 N SER A 104 SHEET 5 AB 6 ASP A 221 VAL A 225 -1 O TYR A 222 N GLY A 148 SHEET 6 AB 6 THR A 189 ASP A 190 -1 O THR A 189 N VAL A 225 SHEET 1 AC 2 TRP A 204 TRP A 205 0 SHEET 2 AC 2 GLY A 217 TRP A 218 -1 N TRP A 218 O TRP A 204 SHEET 1 BA 6 HIS B 55 HIS B 59 0 SHEET 2 BA 6 VAL B 69 SER B 73 -1 O VAL B 69 N HIS B 59 SHEET 3 BA 6 ILE B 31 GLN B 35 -1 O VAL B 32 N TYR B 72 SHEET 4 BA 6 LEU B 2 ASN B 8 1 O LYS B 3 N ILE B 31 SHEET 5 BA 6 LEU B 250 TYR B 254 -1 O LEU B 250 N SER B 6 SHEET 6 BA 6 ALA B 233 VAL B 238 -1 N VAL B 234 O GLU B 253 SHEET 1 BB 6 ASN B 79 ILE B 82 0 SHEET 2 BB 6 PHE B 95 PHE B 100 -1 O ARG B 97 N GLN B 81 SHEET 3 BB 6 LEU B 103 TYR B 109 -1 O LEU B 103 N PHE B 100 SHEET 4 BB 6 ASP B 143 ASP B 149 1 O ASP B 143 N SER B 104 SHEET 5 BB 6 ASP B 221 VAL B 225 -1 O TYR B 222 N GLY B 148 SHEET 6 BB 6 THR B 189 ASP B 190 -1 O THR B 189 N VAL B 225 SHEET 1 BC 2 TRP B 204 TRP B 205 0 SHEET 2 BC 2 GLY B 217 TRP B 218 -1 N TRP B 218 O TRP B 204 SHEET 1 CA 6 HIS C 55 HIS C 59 0 SHEET 2 CA 6 VAL C 69 SER C 73 -1 O VAL C 69 N HIS C 59 SHEET 3 CA 6 ILE C 31 GLN C 35 -1 O VAL C 32 N TYR C 72 SHEET 4 CA 6 LEU C 2 ASN C 8 1 O ILE C 5 N CYS C 33 SHEET 5 CA 6 LEU C 250 TYR C 254 -1 O LEU C 250 N SER C 6 SHEET 6 CA 6 ALA C 233 VAL C 238 -1 N VAL C 234 O GLU C 253 SHEET 1 CB 6 ASN C 79 ILE C 82 0 SHEET 2 CB 6 PHE C 95 PHE C 100 -1 O ARG C 97 N GLN C 81 SHEET 3 CB 6 LEU C 103 TYR C 109 -1 O LEU C 103 N PHE C 100 SHEET 4 CB 6 ASP C 143 ASP C 149 1 O ASP C 143 N SER C 104 SHEET 5 CB 6 ASP C 221 VAL C 225 -1 O TYR C 222 N GLY C 148 SHEET 6 CB 6 THR C 189 ASP C 190 -1 O THR C 189 N VAL C 225 LINK P 3DR U 36 O3' DC U 35 1555 1555 1.61 LINK O3' 3DR U 36 P DC U 37 1555 1555 1.61 LINK P 3DR W 36 O3' DC W 35 1555 1555 1.61 LINK O3' 3DR W 36 P DC W 37 1555 1555 1.61 LINK O3' 3DR Y 36 P DC Y 37 1555 1555 1.61 LINK P 3DR Y 36 O3' DC Y 35 1555 1555 1.61 CRYST1 75.241 75.241 380.683 90.00 90.00 90.00 P 41 21 2 24 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 0.013291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002627 0.00000 MTRIX1 1 -0.069609 0.997532 -0.009240 -45.40930 1 MTRIX2 1 -0.996664 -0.069938 -0.042069 -39.82990 1 MTRIX3 1 -0.042611 0.006281 0.999072 29.60070 1 MTRIX1 2 -0.983417 0.179474 0.026094 -48.19550 1 MTRIX2 2 0.179984 0.983492 0.018689 -32.51940 1 MTRIX3 2 -0.022309 0.023076 -0.999485 -33.04690 1