HEADER HYDROLASE/RNA BINDING PROTEIN 23-JUL-09 3IEY TITLE CRYSTAL STRUCTURE OF THE FUNCTIONAL NANOARCHAEUM EQUITANS TRNA TITLE 2 SPLICING ENDONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-SPLICING ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRNA-INTRON ENDONUCLEASE; COMPND 5 EC: 3.1.27.9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEQ261; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NANOARCHAEUM EQUITANS; SOURCE 3 ORGANISM_TAXID: 160232; SOURCE 4 GENE: ENDA, NEQ205; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-DUET; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: NANOARCHAEUM EQUITANS; SOURCE 12 ORGANISM_TAXID: 160232; SOURCE 13 GENE: NEQ261; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET-DUET KEYWDS PROTEIN HETERODIMER, ENDONUCLEASE, HYDROLASE, NUCLEASE, TRNA KEYWDS 2 PROCESSING, HYDROLASE-RNA BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.MITCHELL,H.LI REVDAT 5 06-SEP-23 3IEY 1 REMARK REVDAT 4 13-OCT-21 3IEY 1 SEQADV REVDAT 3 13-JUL-11 3IEY 1 VERSN REVDAT 2 10-NOV-09 3IEY 1 JRNL REVDAT 1 01-SEP-09 3IEY 0 JRNL AUTH M.MITCHELL,S.XUE,R.ERDMAN,L.RANDAU,D.SOLL,H.LI JRNL TITL CRYSTAL STRUCTURE AND ASSEMBLY OF THE FUNCTIONAL JRNL TITL 2 NANOARCHAEUM EQUITANS TRNA SPLICING ENDONUCLEASE. JRNL REF NUCLEIC ACIDS RES. V. 37 5793 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19578064 JRNL DOI 10.1093/NAR/GKP537 REMARK 2 REMARK 2 RESOLUTION. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 21462 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2347 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 59.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.82000 REMARK 3 B12 (A**2) : 0.00000 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): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.267 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2492 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3345 ; 1.204 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.760 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;34.084 ;23.279 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 478 ;19.061 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;16.745 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1847 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1022 ; 0.188 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1651 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 60 ; 0.099 ; 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): 42 ; 0.133 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.189 ; 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): 1472 ; 0.363 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2300 ; 0.650 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1188 ; 0.868 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1045 ; 1.413 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 7 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 13 REMARK 3 RESIDUE RANGE : A 16 A 37 REMARK 3 RESIDUE RANGE : A 42 A 53 REMARK 3 RESIDUE RANGE : A 54 A 89 REMARK 3 RESIDUE RANGE : A 101 A 154 REMARK 3 RESIDUE RANGE : B 1 B 57 REMARK 3 RESIDUE RANGE : B 58 B 152 REMARK 3 ORIGIN FOR THE GROUP (A): 63.4115 47.6560 -0.7068 REMARK 3 T TENSOR REMARK 3 T11: -0.1505 T22: -0.1220 REMARK 3 T33: -0.0961 T12: 0.0328 REMARK 3 T13: -0.0315 T23: 0.0621 REMARK 3 L TENSOR REMARK 3 L11: 3.2606 L22: 5.4892 REMARK 3 L33: 0.4869 L12: 3.2728 REMARK 3 L13: -0.0392 L23: -0.0755 REMARK 3 S TENSOR REMARK 3 S11: 0.1570 S12: -0.1280 S13: -0.2832 REMARK 3 S21: 0.2089 S22: -0.1356 S23: -0.7063 REMARK 3 S31: 0.0819 S32: 0.0945 S33: -0.0214 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: NULL REMARK 4 REMARK 4 3IEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI 220 SAGITALLY FOCUS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21470 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 11.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.6 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 44.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 FOR SHELL : 3.860 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 1A79 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 44% TACSIMATE, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 62.05100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 62.05100 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.91000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.05100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.45500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.05100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.36500 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 62.05100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.05100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.91000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 62.05100 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.36500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 62.05100 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 17.45500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 124.10200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 124.10200 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 ASP A 14 REMARK 465 LYS A 15 REMARK 465 LYS A 38 REMARK 465 LYS A 39 REMARK 465 LEU A 40 REMARK 465 SER A 41 REMARK 465 LYS B 153 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 A 32 OH TYR A 34 1.86 REMARK 500 NH1 ARG A 97 CB GLU A 101 2.02 REMARK 500 NH1 ARG A 97 CA GLU A 101 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 VAL A 90 CB - CA - C ANGL. DEV. = -25.0 DEGREES REMARK 500 VAL A 90 N - CA - C ANGL. DEV. = 46.9 DEGREES REMARK 500 ILE A 91 N - CA - CB ANGL. DEV. = 37.4 DEGREES REMARK 500 ILE A 91 N - CA - C ANGL. DEV. = -33.1 DEGREES REMARK 500 LYS A 104 CB - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 LYS A 104 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 TRP A 105 N - CA - CB ANGL. DEV. = 15.2 DEGREES REMARK 500 LYS B 58 N - CA - C ANGL. DEV. = 17.7 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 TYR A 34 127.08 -171.66 REMARK 500 ASP A 36 -70.76 -125.63 REMARK 500 VAL A 90 -72.29 -51.90 REMARK 500 LYS A 93 -65.93 139.46 REMARK 500 LYS A 94 -55.10 68.84 REMARK 500 LYS A 96 45.87 -103.74 REMARK 500 ARG A 97 -143.11 91.63 REMARK 500 SER A 98 48.24 -141.63 REMARK 500 GLU A 101 84.14 62.27 REMARK 500 LYS A 104 -3.42 82.91 REMARK 500 TRP A 105 142.59 -175.61 REMARK 500 LYS A 133 -164.05 -118.60 REMARK 500 SER A 141 -154.62 -158.94 REMARK 500 ASN B 59 -28.95 131.88 REMARK 500 PHE B 82 -56.58 -132.77 REMARK 500 ARG B 150 126.38 -174.97 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 LYS A 153 PRO A 154 -48.16 REMARK 500 LYS B 58 ASN B 59 -45.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IF0 RELATED DB: PDB DBREF 3IEY A 1 154 UNP Q74MP4 ENDA_NANEQ 1 154 DBREF 3IEY B 1 153 UNP Q74MS9 Q74MS9_NANEQ 1 153 SEQADV 3IEY MET A 135 UNP Q74MP4 LEU 135 ENGINEERED MUTATION SEQADV 3IEY MET A 137 UNP Q74MP4 LEU 137 ENGINEERED MUTATION SEQRES 1 A 154 MET ILE GLY TYR LEU PHE GLY ASN ARG VAL LEU VAL ASP SEQRES 2 A 154 ASP LYS GLU LEU PRO LEU ILE GLU ALA TYR TYR LEU LEU SEQRES 3 A 154 ASP LYS GLY GLU LEU GLU VAL TYR GLU ASP ASP LYS LYS SEQRES 4 A 154 LEU SER LYS GLU GLU PHE LEU LYS LYS CYS LEU THR TYR SEQRES 5 A 154 ASP GLU ARG PHE LEU ILE ARG TYR LYS ALA TYR LYS GLU SEQRES 6 A 154 LEU ARG ASP LYS GLY TYR THR LEU GLY THR ALA LEU LYS SEQRES 7 A 154 PHE GLY ALA ASP PHE ARG VAL TYR ASP ILE GLY VAL ILE SEQRES 8 A 154 PRO LYS LYS GLY LYS ARG SER GLU ARG GLU HIS SER LYS SEQRES 9 A 154 TRP VAL LEU TYR PRO VAL SER LYS ASP GLU THR PHE ASP SEQRES 10 A 154 PHE TYR GLU PHE ALA SER LYS ASN ARG VAL ALA HIS SER SEQRES 11 A 154 THR ARG LYS LYS MET LEU MET GLY ILE VAL SER ASP LYS SEQRES 12 A 154 ILE GLU PHE ILE GLU VAL SER TRP LYS LYS PRO SEQRES 1 B 153 MET ASN LEU ARG ILE PRO TRP LYS GLU VAL TYR TYR LEU SEQRES 2 B 153 GLY TYR ASN MET GLY ASN TYR ILE LYS ILE SER GLU PRO SEQRES 3 B 153 GLU LEU LEU PHE VAL LEU ARG ASN LYS PRO GLN ILE LYS SEQRES 4 B 153 ASP ARG LEU LYS LEU ASP GLU LYS THR ILE ILE LYS GLU SEQRES 5 B 153 GLY VAL LYS LYS TYR LYS ASN PHE TRP GLU ILE TYR TYR SEQRES 6 B 153 THR VAL LYS ASP LEU ILE LEU ARG GLY TYR ARG VAL ARG SEQRES 7 B 153 PHE ASP GLY PHE PHE ILE GLU LEU TYR GLU LYS GLY ILE SEQRES 8 B 153 ILE PRO GLY THR ILE GLU GLN ASP TYR LEU VAL TYR PRO SEQRES 9 B 153 VAL SER GLY GLU ILE ARG MET THR TRP GLY GLU LEU LEU SEQRES 10 B 153 ASP ILE TYR ASN LYS ALA ILE ALA ARG LYS SER LYS PHE SEQRES 11 B 153 MET LEU ALA ILE VAL ASP SER GLU GLY ASP VAL THR TYR SEQRES 12 B 153 TYR GLU PHE ARG LYS LEU ARG SER ASN LYS HELIX 1 1 LEU A 19 GLY A 29 1 11 HELIX 2 2 LYS A 42 ASP A 53 1 12 HELIX 3 3 ARG A 55 LYS A 69 1 15 HELIX 4 4 LEU A 77 GLY A 80 5 4 HELIX 5 5 PHE A 118 THR A 131 1 14 HELIX 6 6 PRO B 6 TYR B 11 5 6 HELIX 7 7 SER B 24 LYS B 35 1 12 HELIX 8 8 PRO B 36 LYS B 43 1 8 HELIX 9 9 ASP B 45 TYR B 57 1 13 HELIX 10 10 ASN B 59 ARG B 73 1 15 HELIX 11 11 TRP B 113 ARG B 126 1 14 SHEET 1 A 3 TYR A 4 PHE A 6 0 SHEET 2 A 3 ARG A 9 LEU A 11 -1 O ARG A 9 N PHE A 6 SHEET 3 A 3 LEU A 17 PRO A 18 -1 O LEU A 17 N VAL A 10 SHEET 1 B10 THR A 72 ALA A 76 0 SHEET 2 B10 ALA A 81 TYR A 86 -1 O ARG A 84 N GLY A 74 SHEET 3 B10 VAL A 106 SER A 111 -1 O LEU A 107 N PHE A 83 SHEET 4 B10 MET A 135 VAL A 140 1 O LEU A 136 N VAL A 106 SHEET 5 B10 ILE A 144 LYS A 152 -1 O ILE A 147 N MET A 137 SHEET 6 B10 VAL B 141 LYS B 148 -1 O ARG B 147 N GLU A 148 SHEET 7 B10 LYS B 129 VAL B 135 -1 N LEU B 132 O TYR B 144 SHEET 8 B10 TYR B 100 SER B 106 1 N VAL B 105 O ALA B 133 SHEET 9 B10 ILE B 84 TYR B 87 -1 N ILE B 84 O VAL B 102 SHEET 10 B10 ARG B 76 PHE B 79 -1 N ARG B 78 O GLU B 85 SHEET 1 C 2 THR A 115 ASP A 117 0 SHEET 2 C 2 ARG B 110 THR B 112 -1 O MET B 111 N PHE A 116 SHEET 1 D 3 ASN B 2 LEU B 3 0 SHEET 2 D 3 ILE B 21 LYS B 22 -1 O ILE B 21 N LEU B 3 SHEET 3 D 3 TYR B 15 ASN B 16 -1 N TYR B 15 O LYS B 22 CISPEP 1 VAL A 90 ILE A 91 0 -11.96 CISPEP 2 ARG A 97 SER A 98 0 -6.15 CISPEP 3 SER B 151 ASN B 152 0 0.54 CRYST1 124.102 124.102 69.820 90.00 90.00 90.00 I 41 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 0.008058 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014323 0.00000