HEADER HYDROLASE/DNA 07-JUN-06 2H8C TITLE STRUCTURE OF RUSA D70N IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'; COMPND 3 CHAIN: Y, Z, W, X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUSA; COMPND 7 CHAIN: A, B, C, D; COMPND 8 SYNONYM: HOLLIDAY JUNCTION NUCLEASE RUSA, HOLLIDAY JUNCTION COMPND 9 RESOLVASE; COMPND 10 EC: 3.1.22.-; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 5 ORGANISM_TAXID: 562; SOURCE 6 GENE: RUSA, RUS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-DNA COMPLEX, RECOMBINATION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.A.MACMASTER REVDAT 5 30-AUG-23 2H8C 1 REMARK REVDAT 4 20-OCT-21 2H8C 1 SEQADV REVDAT 3 13-JUL-11 2H8C 1 VERSN REVDAT 2 24-FEB-09 2H8C 1 VERSN REVDAT 1 24-APR-07 2H8C 0 JRNL AUTH R.MACMASTER,S.SEDELNIKOVA,P.J.BAKER,E.L.BOLT,R.G.LLOYD, JRNL AUTH 2 J.B.RAFFERTY JRNL TITL RUSA HOLLIDAY JUNCTION RESOLVASE: DNA COMPLEX JRNL TITL 2 STRUCTURE--INSIGHTS INTO SELECTIVITY AND SPECIFICITY. JRNL REF NUCLEIC ACIDS RES. V. 34 5577 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 17028102 JRNL DOI 10.1093/NAR/GKL447 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11874 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 850 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4520 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.4740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3474 REMARK 3 NUCLEIC ACID ATOMS : 868 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.66000 REMARK 3 B22 (A**2) : 5.26000 REMARK 3 B33 (A**2) : -8.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.94000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.551 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.525 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 66.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.843 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4561 ; 0.004 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6400 ; 0.922 ; 2.197 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 452 ;10.095 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 153 ;39.931 ;23.399 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 554 ;22.792 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;22.220 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 719 ; 0.045 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3392 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2393 ; 0.304 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2966 ; 0.335 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 207 ; 0.211 ; 0.200 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): 49 ; 0.312 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.397 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 118 REMARK 3 RESIDUE RANGE : B 2 B 117 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9268 1.4075 3.6776 REMARK 3 T TENSOR REMARK 3 T11: -0.3528 T22: -0.2509 REMARK 3 T33: -0.4494 T12: 0.1031 REMARK 3 T13: 0.0404 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 5.4088 L22: 3.3200 REMARK 3 L33: 7.8961 L12: 1.1609 REMARK 3 L13: 0.6834 L23: 1.5910 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: 0.0629 S13: 0.0449 REMARK 3 S21: -0.0989 S22: 0.0534 S23: -0.3898 REMARK 3 S31: 0.1898 S32: 0.9308 S33: -0.0834 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 118 REMARK 3 RESIDUE RANGE : D 2 D 118 REMARK 3 ORIGIN FOR THE GROUP (A): 41.1796 17.4087 52.0249 REMARK 3 T TENSOR REMARK 3 T11: 0.0253 T22: -0.1431 REMARK 3 T33: -0.4287 T12: -0.0495 REMARK 3 T13: -0.1627 T23: 0.1191 REMARK 3 L TENSOR REMARK 3 L11: 4.1450 L22: 7.1312 REMARK 3 L33: 9.1083 L12: -0.9643 REMARK 3 L13: -0.3827 L23: -2.6614 REMARK 3 S TENSOR REMARK 3 S11: 0.1024 S12: 0.0822 S13: -0.0242 REMARK 3 S21: 0.1282 S22: 0.0201 S23: -0.3074 REMARK 3 S31: -0.4992 S32: -0.2526 S33: -0.1226 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : W 2 W 12 REMARK 3 RESIDUE RANGE : X 2 X 12 REMARK 3 ORIGIN FOR THE GROUP (A): 5.2600 21.5676 22.9458 REMARK 3 T TENSOR REMARK 3 T11: -0.1094 T22: -0.0141 REMARK 3 T33: -0.5146 T12: -0.0667 REMARK 3 T13: -0.0732 T23: -0.1533 REMARK 3 L TENSOR REMARK 3 L11: 1.1584 L22: 19.2723 REMARK 3 L33: 2.1426 L12: -1.3380 REMARK 3 L13: -0.8072 L23: 6.2249 REMARK 3 S TENSOR REMARK 3 S11: -0.0534 S12: -0.5642 S13: -0.0151 REMARK 3 S21: 0.9082 S22: -0.2474 S23: 0.5604 REMARK 3 S31: 0.1354 S32: -0.3166 S33: 0.3007 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Y 2 Y 12 REMARK 3 RESIDUE RANGE : Z 2 Z 11 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5697 22.9977 25.3321 REMARK 3 T TENSOR REMARK 3 T11: 0.2208 T22: 0.4892 REMARK 3 T33: -0.1095 T12: -0.0623 REMARK 3 T13: 0.0987 T23: 0.1837 REMARK 3 L TENSOR REMARK 3 L11: 5.1998 L22: 3.9080 REMARK 3 L33: 21.8599 L12: 2.4075 REMARK 3 L13: -4.1430 L23: -6.8182 REMARK 3 S TENSOR REMARK 3 S11: -0.3668 S12: 0.4093 S13: -0.3591 REMARK 3 S21: 0.2985 S22: 0.4793 S23: 0.3043 REMARK 3 S31: 0.4728 S32: -2.0688 S33: -0.1125 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 2H8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12485 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PDB ENTRY 1Q8R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M SODIUM FLUORIDE, PH REMARK 280 7.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 7.10 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.74150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: W, X, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Y, Z, C, D 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 DT Z 12 REMARK 465 MET A 1 REMARK 465 ASN A 119 REMARK 465 GLU A 120 REMARK 465 MET B 1 REMARK 465 GLY B 118 REMARK 465 ASN B 119 REMARK 465 GLU B 120 REMARK 465 MET C 1 REMARK 465 ASN C 21 REMARK 465 ARG C 22 REMARK 465 GLY C 23 REMARK 465 ARG C 24 REMARK 465 THR C 25 REMARK 465 HIS C 26 REMARK 465 ASN C 119 REMARK 465 GLU C 120 REMARK 465 MET D 1 REMARK 465 HIS D 20 REMARK 465 ASN D 21 REMARK 465 ARG D 22 REMARK 465 GLY D 23 REMARK 465 ARG D 24 REMARK 465 ASN D 119 REMARK 465 GLU D 120 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 ASN A 15 CG OD1 ND2 REMARK 470 HIS A 20 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 21 CG OD1 ND2 REMARK 470 ARG A 66 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 101 CE NZ REMARK 470 ASN B 2 CG OD1 ND2 REMARK 470 ARG B 19 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 20 CG ND1 CD2 CE1 NE2 REMARK 470 ASN B 21 CG OD1 ND2 REMARK 470 ARG B 22 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 ARG B 66 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 76 CD CE NZ REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 GLU B 116 CG CD OE1 OE2 REMARK 470 ASN C 2 OD1 ND2 REMARK 470 LEU C 8 CG CD1 CD2 REMARK 470 ARG C 16 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 19 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 37 CG OD1 ND2 REMARK 470 ILE C 41 CG1 CG2 CD1 REMARK 470 LYS C 43 CG CD CE NZ REMARK 470 LEU C 47 CG CD1 CD2 REMARK 470 LYS C 56 CD CE NZ REMARK 470 ARG C 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 68 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 69 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 76 CD CE NZ REMARK 470 LYS C 84 CD CE NZ REMARK 470 LYS C 101 CD CE NZ REMARK 470 GLU C 116 CG CD OE1 OE2 REMARK 470 ASN D 2 OD1 ND2 REMARK 470 SER D 13 OG REMARK 470 ARG D 16 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 19 CG CD NE CZ NH1 NH2 REMARK 470 TYR D 34 CD1 REMARK 470 ARG D 40 CD NE CZ NH1 NH2 REMARK 470 ILE D 42 CG1 CG2 CD1 REMARK 470 LYS D 43 CD CE NZ REMARK 470 ARG D 66 CZ NH1 NH2 REMARK 470 ARG D 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 76 CG CD CE NZ REMARK 470 LYS D 106 CG CD CE NZ REMARK 470 ARG D 109 CG CD NE CZ NH1 NH2 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 OD2 ASP B 65 NH2 ARG B 69 2.07 REMARK 500 O ILE B 42 N MET B 46 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OP1 DC X 3 NE ARG A 109 2555 2.12 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 DC Y 3 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DT Y 6 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC Y 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG Z 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DT Z 6 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC Z 9 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DC W 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC W 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG X 4 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG X 4 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA X 7 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DC X 8 O4' - C1' - N1 ANGL. DEV. = 5.3 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 15 -23.11 -39.84 REMARK 500 ARG A 22 50.52 21.89 REMARK 500 ARG A 24 -175.99 -64.88 REMARK 500 ALA A 45 13.96 -63.10 REMARK 500 MET A 46 24.75 44.56 REMARK 500 ASP A 48 53.53 -69.55 REMARK 500 ASP A 65 -172.72 178.17 REMARK 500 ASP A 96 111.81 -176.39 REMARK 500 GLU A 116 -164.22 -63.05 REMARK 500 MET A 117 16.90 174.45 REMARK 500 SER B 13 125.00 -36.18 REMARK 500 ASN B 14 -17.31 -48.77 REMARK 500 ARG B 19 -163.40 -162.13 REMARK 500 HIS B 20 -44.86 -139.40 REMARK 500 ASN B 21 -151.90 -81.74 REMARK 500 ARG B 22 99.22 -59.77 REMARK 500 GLN B 32 -67.84 -29.91 REMARK 500 TYR B 34 -74.86 -52.57 REMARK 500 ARG B 35 -57.82 -18.38 REMARK 500 ASP B 36 -73.72 -56.32 REMARK 500 ASN B 37 -9.99 -42.88 REMARK 500 VAL B 38 -65.72 -96.17 REMARK 500 MET B 46 37.81 77.86 REMARK 500 LEU B 47 40.99 -104.32 REMARK 500 LEU B 51 124.61 -39.42 REMARK 500 ASP B 65 -166.63 -171.81 REMARK 500 LEU B 89 -90.16 -90.05 REMARK 500 VAL B 94 98.54 -65.71 REMARK 500 ASP B 96 108.06 -161.85 REMARK 500 ASN C 14 -86.47 -17.59 REMARK 500 ASN C 15 -68.20 11.64 REMARK 500 TYR C 17 -19.09 -40.38 REMARK 500 GLN C 32 -70.06 -45.08 REMARK 500 ALA C 45 7.06 -67.92 REMARK 500 ASP C 48 37.49 -92.73 REMARK 500 ALA C 52 -66.72 -99.86 REMARK 500 MET C 53 -165.46 -53.19 REMARK 500 ALA C 78 -70.82 -44.92 REMARK 500 ALA C 81 -73.81 -52.63 REMARK 500 LEU C 82 -59.24 -19.12 REMARK 500 ALA C 85 13.98 -69.54 REMARK 500 PHE C 87 -72.47 -73.22 REMARK 500 ALA C 92 -16.27 -49.91 REMARK 500 ASP C 96 107.40 -162.54 REMARK 500 LYS C 106 116.81 -38.68 REMARK 500 PRO D 9 -129.84 -51.36 REMARK 500 PRO D 12 151.23 -47.00 REMARK 500 VAL D 27 -149.33 -73.32 REMARK 500 ALA D 29 -67.49 -26.81 REMARK 500 ALA D 45 -8.61 -59.42 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. 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 ARG B 19 HIS B 20 -55.17 REMARK 500 ASP C 48 ILE C 49 -148.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H8E RELATED DB: PDB REMARK 900 STRUCTURE OF RUSA D70N DBREF 2H8C A 1 120 UNP P0AG74 RUS_ECOLI 1 120 DBREF 2H8C B 1 120 UNP P0AG74 RUS_ECOLI 1 120 DBREF 2H8C C 1 120 UNP P0AG74 RUS_ECOLI 1 120 DBREF 2H8C D 1 120 UNP P0AG74 RUS_ECOLI 1 120 DBREF 2H8C Y 2 12 PDB 2H8C 2H8C 2 12 DBREF 2H8C Z 2 12 PDB 2H8C 2H8C 2 12 DBREF 2H8C W 2 12 PDB 2H8C 2H8C 2 12 DBREF 2H8C X 2 12 PDB 2H8C 2H8C 2 12 SEQADV 2H8C ASN A 70 UNP P0AG74 ASP 70 ENGINEERED MUTATION SEQADV 2H8C ASN B 70 UNP P0AG74 ASP 70 ENGINEERED MUTATION SEQADV 2H8C ASN C 70 UNP P0AG74 ASP 70 ENGINEERED MUTATION SEQADV 2H8C ASN D 70 UNP P0AG74 ASP 70 ENGINEERED MUTATION SEQRES 1 Y 11 DC DC DG DG DT DA DC DC DG DG DT SEQRES 1 Z 11 DC DC DG DG DT DA DC DC DG DG DT SEQRES 1 W 11 DC DC DG DG DT DA DC DC DG DG DT SEQRES 1 X 11 DC DC DG DG DT DA DC DC DG DG DT SEQRES 1 A 120 MET ASN THR TYR SER ILE THR LEU PRO TRP PRO PRO SER SEQRES 2 A 120 ASN ASN ARG TYR TYR ARG HIS ASN ARG GLY ARG THR HIS SEQRES 3 A 120 VAL SER ALA GLU GLY GLN ALA TYR ARG ASP ASN VAL ALA SEQRES 4 A 120 ARG ILE ILE LYS ASN ALA MET LEU ASP ILE GLY LEU ALA SEQRES 5 A 120 MET PRO VAL LYS ILE ARG ILE GLU CYS HIS MET PRO ASP SEQRES 6 A 120 ARG ARG ARG ARG ASN LEU ASP ASN LEU GLN LYS ALA ALA SEQRES 7 A 120 PHE ASP ALA LEU THR LYS ALA GLY PHE TRP LEU ASP ASP SEQRES 8 A 120 ALA GLN VAL VAL ASP TYR ARG VAL VAL LYS MET PRO VAL SEQRES 9 A 120 THR LYS GLY GLY ARG LEU GLU LEU THR ILE THR GLU MET SEQRES 10 A 120 GLY ASN GLU SEQRES 1 B 120 MET ASN THR TYR SER ILE THR LEU PRO TRP PRO PRO SER SEQRES 2 B 120 ASN ASN ARG TYR TYR ARG HIS ASN ARG GLY ARG THR HIS SEQRES 3 B 120 VAL SER ALA GLU GLY GLN ALA TYR ARG ASP ASN VAL ALA SEQRES 4 B 120 ARG ILE ILE LYS ASN ALA MET LEU ASP ILE GLY LEU ALA SEQRES 5 B 120 MET PRO VAL LYS ILE ARG ILE GLU CYS HIS MET PRO ASP SEQRES 6 B 120 ARG ARG ARG ARG ASN LEU ASP ASN LEU GLN LYS ALA ALA SEQRES 7 B 120 PHE ASP ALA LEU THR LYS ALA GLY PHE TRP LEU ASP ASP SEQRES 8 B 120 ALA GLN VAL VAL ASP TYR ARG VAL VAL LYS MET PRO VAL SEQRES 9 B 120 THR LYS GLY GLY ARG LEU GLU LEU THR ILE THR GLU MET SEQRES 10 B 120 GLY ASN GLU SEQRES 1 C 120 MET ASN THR TYR SER ILE THR LEU PRO TRP PRO PRO SER SEQRES 2 C 120 ASN ASN ARG TYR TYR ARG HIS ASN ARG GLY ARG THR HIS SEQRES 3 C 120 VAL SER ALA GLU GLY GLN ALA TYR ARG ASP ASN VAL ALA SEQRES 4 C 120 ARG ILE ILE LYS ASN ALA MET LEU ASP ILE GLY LEU ALA SEQRES 5 C 120 MET PRO VAL LYS ILE ARG ILE GLU CYS HIS MET PRO ASP SEQRES 6 C 120 ARG ARG ARG ARG ASN LEU ASP ASN LEU GLN LYS ALA ALA SEQRES 7 C 120 PHE ASP ALA LEU THR LYS ALA GLY PHE TRP LEU ASP ASP SEQRES 8 C 120 ALA GLN VAL VAL ASP TYR ARG VAL VAL LYS MET PRO VAL SEQRES 9 C 120 THR LYS GLY GLY ARG LEU GLU LEU THR ILE THR GLU MET SEQRES 10 C 120 GLY ASN GLU SEQRES 1 D 120 MET ASN THR TYR SER ILE THR LEU PRO TRP PRO PRO SER SEQRES 2 D 120 ASN ASN ARG TYR TYR ARG HIS ASN ARG GLY ARG THR HIS SEQRES 3 D 120 VAL SER ALA GLU GLY GLN ALA TYR ARG ASP ASN VAL ALA SEQRES 4 D 120 ARG ILE ILE LYS ASN ALA MET LEU ASP ILE GLY LEU ALA SEQRES 5 D 120 MET PRO VAL LYS ILE ARG ILE GLU CYS HIS MET PRO ASP SEQRES 6 D 120 ARG ARG ARG ARG ASN LEU ASP ASN LEU GLN LYS ALA ALA SEQRES 7 D 120 PHE ASP ALA LEU THR LYS ALA GLY PHE TRP LEU ASP ASP SEQRES 8 D 120 ALA GLN VAL VAL ASP TYR ARG VAL VAL LYS MET PRO VAL SEQRES 9 D 120 THR LYS GLY GLY ARG LEU GLU LEU THR ILE THR GLU MET SEQRES 10 D 120 GLY ASN GLU FORMUL 9 HOH *2(H2 O) HELIX 1 1 SER A 13 TYR A 17 1 5 HELIX 2 2 SER A 28 ALA A 45 1 18 HELIX 3 3 ASN A 70 GLY A 86 1 17 HELIX 4 4 SER B 13 TYR B 17 1 5 HELIX 5 5 SER B 28 MET B 46 1 19 HELIX 6 6 LEU B 71 ALA B 85 1 15 HELIX 7 7 ASP B 90 ALA B 92 5 3 HELIX 8 8 SER C 13 TYR C 18 1 6 HELIX 9 9 SER C 28 LYS C 43 1 16 HELIX 10 10 ASN C 70 ALA C 85 1 16 HELIX 11 11 ASP C 90 ALA C 92 5 3 HELIX 12 12 SER D 13 TYR D 18 1 6 HELIX 13 13 SER D 28 ALA D 45 1 18 HELIX 14 14 ASN D 70 ALA D 85 1 16 HELIX 15 15 ASP D 90 ALA D 92 5 3 SHEET 1 A 8 THR A 3 PRO A 9 0 SHEET 2 A 8 ARG A 109 THR A 115 -1 O LEU A 112 N ILE A 6 SHEET 3 A 8 VAL A 55 HIS A 62 -1 N GLU A 60 O GLU A 111 SHEET 4 A 8 VAL A 94 MET A 102 1 O VAL A 100 N CYS A 61 SHEET 5 A 8 VAL B 94 MET B 102 -1 O VAL B 95 N LYS A 101 SHEET 6 A 8 VAL B 55 HIS B 62 1 N ILE B 59 O ARG B 98 SHEET 7 A 8 ARG B 109 GLU B 116 -1 O GLU B 111 N GLU B 60 SHEET 8 A 8 THR B 3 PRO B 9 -1 N TYR B 4 O ILE B 114 SHEET 1 B 2 TYR A 18 HIS A 20 0 SHEET 2 B 2 THR A 25 VAL A 27 -1 O HIS A 26 N ARG A 19 SHEET 1 C 2 TYR B 18 ARG B 19 0 SHEET 2 C 2 HIS B 26 VAL B 27 -1 O HIS B 26 N ARG B 19 SHEET 1 D 8 THR C 3 PRO C 9 0 SHEET 2 D 8 ARG C 109 GLU C 116 -1 O LEU C 112 N ILE C 6 SHEET 3 D 8 VAL C 55 HIS C 62 -1 N GLU C 60 O GLU C 111 SHEET 4 D 8 VAL C 94 MET C 102 1 O VAL C 100 N CYS C 61 SHEET 5 D 8 VAL D 94 MET D 102 -1 O LYS D 101 N VAL C 95 SHEET 6 D 8 VAL D 55 HIS D 62 1 N CYS D 61 O MET D 102 SHEET 7 D 8 ARG D 109 GLU D 116 -1 O ARG D 109 N HIS D 62 SHEET 8 D 8 THR D 3 LEU D 8 -1 N ILE D 6 O LEU D 112 CRYST1 64.616 59.483 90.721 90.00 101.59 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015476 0.000000 0.003174 0.00000 SCALE2 0.000000 0.016812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011252 0.00000