HEADER SPLICING 30-JAN-09 2ZYZ TITLE PYROBACULUM AEROPHILUM SPLICING ENDONUCLEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PAE0789; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: SPLICING ENDONUCLEASE STRUCTURAL SUBUNIT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TRNA-SPLICING ENDONUCLEASE; COMPND 8 CHAIN: B, D; COMPND 9 SYNONYM: SPLICING ENDONUCLEASE CATALYTIC SUBUNIT, TRNA-INTRON COMPND 10 ENDONUCLEASE; COMPND 11 EC: 3.1.27.9; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROBACULUM AEROPHILUM; SOURCE 3 ORGANISM_TAXID: 13773; SOURCE 4 STRAIN: IM2; SOURCE 5 GENE: PAE0789; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-PAE-ENDA; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: PYROBACULUM AEROPHILUM; SOURCE 13 ORGANISM_TAXID: 13773; SOURCE 14 STRAIN: IM2; SOURCE 15 GENE: PAE2269; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PETDUET-PAE-ENDA KEYWDS SPLICING ENDONUCLEASE, CRENARCHAEA, HETEROTETRAMER, RNA PROCESSING, KEYWDS 2 ENDONUCLEASE, HYDROLASE, NUCLEASE, TRNA PROCESSING, SPLICING EXPDTA X-RAY DIFFRACTION AUTHOR S.YOSHINARI,D.K.INAOKA,Y.WATANABE,T.SHIBA,G.KURISU,S.HARADA REVDAT 4 13-MAR-24 2ZYZ 1 SEQADV REVDAT 3 25-JAN-12 2ZYZ 1 VERSN SOURCE REVDAT 2 01-SEP-09 2ZYZ 1 JRNL REVDAT 1 23-JUN-09 2ZYZ 0 JRNL AUTH S.YOSHINARI,T.SHIBA,D.K.INAOKA,T.ITOH,G.KURISU,S.HARADA, JRNL AUTH 2 K.KITA,Y.WATANABE JRNL TITL FUNCTIONAL IMPORTANCE OF CRENARCHAEA-SPECIFIC EXTRA-LOOP JRNL TITL 2 REVEALED BY AN X-RAY STRUCTURE OF A HETEROTETRAMERIC JRNL TITL 3 CRENARCHAEAL SPLICING ENDONUCLEASE JRNL REF NUCLEIC ACIDS RES. V. 37 4787 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19515941 JRNL DOI 10.1093/NAR/GKP506 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 65559 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3500 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4656 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 233 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4479 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 443 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.91 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.125 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.429 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4885 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6612 ; 1.711 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 625 ; 7.666 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;34.194 ;22.679 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 948 ;16.451 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.488 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 732 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3650 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2350 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3349 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 380 ; 0.120 ; 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): 54 ; 0.181 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.242 ; 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): 2986 ; 1.147 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4707 ; 1.891 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2153 ; 2.524 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1877 ; 3.753 ; 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 : 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: NULL REMARK 4 REMARK 4 2ZYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000028602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M LISO4, 15% PEG8000, PH 8.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 34.88100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.51200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.36300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.51200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.88100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.36300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 GLU A 94 REMARK 465 ALA A 95 REMARK 465 VAL A 96 REMARK 465 MET C -19 REMARK 465 GLY C -18 REMARK 465 SER C -17 REMARK 465 SER C -16 REMARK 465 HIS C -15 REMARK 465 HIS C -14 REMARK 465 HIS C -13 REMARK 465 HIS C -12 REMARK 465 HIS C -11 REMARK 465 HIS C -10 REMARK 465 SER C -9 REMARK 465 SER C -8 REMARK 465 GLY C -7 REMARK 465 LEU C -6 REMARK 465 VAL C -5 REMARK 465 PRO C -4 REMARK 465 ARG C -3 REMARK 465 GLY C -2 REMARK 465 SER C -1 REMARK 465 HIS C 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 86 CG ARG B 86 CD -0.191 REMARK 500 TYR C 36 CD1 TYR C 36 CE1 -0.093 REMARK 500 TYR D 22 CD1 TYR D 22 CE1 -0.092 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 ASP A 2 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLU A 34 N - CA - CB ANGL. DEV. = 16.1 DEGREES REMARK 500 GLU A 34 N - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 ASP B 127 N - CA - C ANGL. DEV. = -16.5 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 LYS A 26 -14.05 77.36 REMARK 500 LYS A 33 -25.15 77.22 REMARK 500 PRO B 124 -74.87 -59.74 REMARK 500 HIS B 128 79.93 59.82 REMARK 500 ALA B 129 88.66 99.78 REMARK 500 LYS C 26 -2.40 80.77 REMARK 500 LYS C 32 -88.84 -125.23 REMARK 500 GLU D 24 53.20 -93.62 REMARK 500 ILE D 126 -122.48 -141.71 REMARK 500 ASP D 127 93.10 -170.02 REMARK 500 HIS D 128 -97.68 -155.52 REMARK 500 ALA D 129 75.16 43.53 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 LEU B 31 GLY B 32 -32.48 REMARK 500 LYS B 61 GLY B 62 -78.61 REMARK 500 HIS B 128 ALA B 129 46.36 REMARK 500 MET C 1 ASP C 2 131.34 REMARK 500 ILE D 126 ASP D 127 31.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 33 -13.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 2ZYZ A 1 96 UNP Q8ZYG6 Q8ZYG6_PYRAE 1 96 DBREF 2ZYZ B 1 183 UNP Q8ZVI1 ENDA_PYRAE 1 183 DBREF 2ZYZ C 1 96 UNP Q8ZYG6 Q8ZYG6_PYRAE 1 96 DBREF 2ZYZ D 1 183 UNP Q8ZVI1 ENDA_PYRAE 1 183 SEQADV 2ZYZ MET A -19 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY A -18 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER A -17 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER A -16 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -15 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -14 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -13 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -12 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -11 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A -10 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER A -9 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER A -8 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY A -7 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ LEU A -6 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ VAL A -5 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ PRO A -4 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ ARG A -3 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY A -2 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER A -1 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS A 0 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ MET C -19 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY C -18 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER C -17 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER C -16 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -15 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -14 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -13 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -12 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -11 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C -10 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER C -9 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER C -8 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY C -7 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ LEU C -6 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ VAL C -5 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ PRO C -4 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ ARG C -3 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ GLY C -2 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ SER C -1 UNP Q8ZYG6 EXPRESSION TAG SEQADV 2ZYZ HIS C 0 UNP Q8ZYG6 EXPRESSION TAG SEQRES 1 A 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 116 LEU VAL PRO ARG GLY SER HIS MET ASP VAL LEU GLN GLU SEQRES 3 A 116 GLN VAL PHE LYS ASP LEU LYS SER ARG GLY PHE LYS ILE SEQRES 4 A 116 ILE GLU GLN LEU ASP ASP LYS ILE PHE ILE ALA GLU LYS SEQRES 5 A 116 LYS GLU ARG TYR LEU PHE TYR VAL MET VAL GLU GLY VAL SEQRES 6 A 116 GLU VAL THR ILE GLN THR LEU LEU SER VAL ILE ASN MET SEQRES 7 A 116 GLY GLU THR LEU SER MET PRO VAL VAL LEU ALA LEU VAL SEQRES 8 A 116 SER ASN ASP GLY THR VAL THR TYR TYR TYR VAL ARG LYS SEQRES 9 A 116 ILE ARG LEU PRO ARG ASN ILE TYR ALA GLU ALA VAL SEQRES 1 B 183 MET ILE GLY TYR LEU ARG GLY LEU ALA VAL ILE VAL GLU SEQRES 2 B 183 ASP VAL GLU PHE ALA ARG ARG LEU TYR LYS GLU GLY PHE SEQRES 3 B 183 TYR GLY ARG PHE LEU GLY TYR ASP LYS VAL LYS ARG ASP SEQRES 4 B 183 GLU VAL GLU LYS ILE ASN ALA PRO LEU ILE LEU GLY LEU SEQRES 5 B 183 TYR GLU ALA LEU TYR LEU ALA GLU LYS GLY ARG LEU LYS SEQRES 6 B 183 VAL MET GLY GLU ASP GLY ARG GLU VAL ALA PRO GLU GLU SEQRES 7 B 183 LEU ALA ALA LEU GLY ARG GLU ARG MET ARG ASN PHE ASP SEQRES 8 B 183 GLU ILE TYR LYS ILE TYR LYS TYR PHE ARG ASP LEU GLY SEQRES 9 B 183 TYR VAL VAL LYS SER GLY LEU LYS PHE GLY ALA LEU PHE SEQRES 10 B 183 SER VAL TYR GLU LYS GLY PRO GLY ILE ASP HIS ALA PRO SEQRES 11 B 183 MET VAL VAL VAL PHE LEU GLU PRO ASP LYS GLY ILE SER SEQRES 12 B 183 ALA THR ASP ILE THR ARG GLY GLY ARG LEU SER HIS SER SEQRES 13 B 183 VAL ARG LYS THR TRP THR LEU ALA THR VAL LEU ARG GLN SEQRES 14 B 183 THR GLY GLU VAL VAL LEU LEU GLY PHE GLY TRP ALA ARG SEQRES 15 B 183 LEU SEQRES 1 C 116 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 C 116 LEU VAL PRO ARG GLY SER HIS MET ASP VAL LEU GLN GLU SEQRES 3 C 116 GLN VAL PHE LYS ASP LEU LYS SER ARG GLY PHE LYS ILE SEQRES 4 C 116 ILE GLU GLN LEU ASP ASP LYS ILE PHE ILE ALA GLU LYS SEQRES 5 C 116 LYS GLU ARG TYR LEU PHE TYR VAL MET VAL GLU GLY VAL SEQRES 6 C 116 GLU VAL THR ILE GLN THR LEU LEU SER VAL ILE ASN MET SEQRES 7 C 116 GLY GLU THR LEU SER MET PRO VAL VAL LEU ALA LEU VAL SEQRES 8 C 116 SER ASN ASP GLY THR VAL THR TYR TYR TYR VAL ARG LYS SEQRES 9 C 116 ILE ARG LEU PRO ARG ASN ILE TYR ALA GLU ALA VAL SEQRES 1 D 183 MET ILE GLY TYR LEU ARG GLY LEU ALA VAL ILE VAL GLU SEQRES 2 D 183 ASP VAL GLU PHE ALA ARG ARG LEU TYR LYS GLU GLY PHE SEQRES 3 D 183 TYR GLY ARG PHE LEU GLY TYR ASP LYS VAL LYS ARG ASP SEQRES 4 D 183 GLU VAL GLU LYS ILE ASN ALA PRO LEU ILE LEU GLY LEU SEQRES 5 D 183 TYR GLU ALA LEU TYR LEU ALA GLU LYS GLY ARG LEU LYS SEQRES 6 D 183 VAL MET GLY GLU ASP GLY ARG GLU VAL ALA PRO GLU GLU SEQRES 7 D 183 LEU ALA ALA LEU GLY ARG GLU ARG MET ARG ASN PHE ASP SEQRES 8 D 183 GLU ILE TYR LYS ILE TYR LYS TYR PHE ARG ASP LEU GLY SEQRES 9 D 183 TYR VAL VAL LYS SER GLY LEU LYS PHE GLY ALA LEU PHE SEQRES 10 D 183 SER VAL TYR GLU LYS GLY PRO GLY ILE ASP HIS ALA PRO SEQRES 11 D 183 MET VAL VAL VAL PHE LEU GLU PRO ASP LYS GLY ILE SER SEQRES 12 D 183 ALA THR ASP ILE THR ARG GLY GLY ARG LEU SER HIS SER SEQRES 13 D 183 VAL ARG LYS THR TRP THR LEU ALA THR VAL LEU ARG GLN SEQRES 14 D 183 THR GLY GLU VAL VAL LEU LEU GLY PHE GLY TRP ALA ARG SEQRES 15 D 183 LEU FORMUL 5 HOH *443(H2 O) HELIX 1 1 ASP A 2 SER A 14 1 13 HELIX 2 2 THR A 48 SER A 63 1 16 HELIX 3 3 ASP B 14 GLU B 24 1 11 HELIX 4 4 LYS B 37 ILE B 44 5 8 HELIX 5 5 LEU B 52 LYS B 61 1 10 HELIX 6 6 ALA B 75 MET B 87 1 13 HELIX 7 7 ASN B 89 LEU B 103 1 15 HELIX 8 8 LEU B 111 GLY B 114 5 4 HELIX 9 9 SER B 143 SER B 154 1 12 HELIX 10 10 ASP C 2 ARG C 15 1 14 HELIX 11 11 THR C 48 LEU C 62 1 15 HELIX 12 12 ASP D 14 GLU D 24 1 11 HELIX 13 13 ASP D 39 ILE D 44 5 6 HELIX 14 14 LEU D 52 LYS D 61 1 10 HELIX 15 15 ALA D 75 MET D 87 1 13 HELIX 16 16 ASN D 89 LEU D 103 1 15 HELIX 17 17 LEU D 111 GLY D 114 5 4 HELIX 18 18 SER D 143 SER D 154 1 12 SHEET 1 A10 LYS A 18 ASP A 24 0 SHEET 2 A10 ILE A 27 GLU A 31 -1 O ILE A 29 N GLU A 21 SHEET 3 A10 ARG A 35 VAL A 42 -1 O PHE A 38 N PHE A 28 SHEET 4 A10 VAL A 66 VAL A 71 1 O ALA A 69 N MET A 41 SHEET 5 A10 VAL A 77 LYS A 84 -1 O THR A 78 N LEU A 70 SHEET 6 A10 VAL B 173 TRP B 180 -1 O GLY B 179 N TYR A 81 SHEET 7 A10 TRP B 161 VAL B 166 -1 N THR B 165 O VAL B 174 SHEET 8 A10 MET B 131 PHE B 135 1 N VAL B 134 O ALA B 164 SHEET 9 A10 PHE B 117 TYR B 120 -1 N PHE B 117 O VAL B 133 SHEET 10 A10 VAL B 106 SER B 109 -1 N LYS B 108 O SER B 118 SHEET 1 B 6 ARG B 29 PHE B 30 0 SHEET 2 B 6 LEU B 48 GLY B 51 -1 O ILE B 49 N ARG B 29 SHEET 3 B 6 ALA B 9 VAL B 12 -1 N VAL B 10 O LEU B 50 SHEET 4 B 6 ILE B 2 LEU B 5 -1 N TYR B 4 O ILE B 11 SHEET 5 B 6 LYS B 65 MET B 67 1 O MET B 67 N GLY B 3 SHEET 6 B 6 GLU B 73 VAL B 74 -1 O VAL B 74 N VAL B 66 SHEET 1 C10 LYS C 18 ASP C 24 0 SHEET 2 C10 ILE C 27 GLU C 31 -1 O ILE C 29 N ILE C 20 SHEET 3 C10 ARG C 35 VAL C 42 -1 O PHE C 38 N PHE C 28 SHEET 4 C10 VAL C 66 VAL C 71 1 O ALA C 69 N TYR C 39 SHEET 5 C10 VAL C 77 LYS C 84 -1 O THR C 78 N LEU C 70 SHEET 6 C10 VAL D 173 TRP D 180 -1 O GLY D 177 N ARG C 83 SHEET 7 C10 TRP D 161 VAL D 166 -1 N TRP D 161 O PHE D 178 SHEET 8 C10 MET D 131 PHE D 135 1 N VAL D 134 O THR D 162 SHEET 9 C10 PHE D 117 TYR D 120 -1 N VAL D 119 O MET D 131 SHEET 10 C10 VAL D 106 SER D 109 -1 N LYS D 108 O SER D 118 SHEET 1 D 5 ARG D 29 PHE D 30 0 SHEET 2 D 5 LEU D 48 GLY D 51 -1 O ILE D 49 N ARG D 29 SHEET 3 D 5 ALA D 9 VAL D 12 -1 N VAL D 10 O LEU D 50 SHEET 4 D 5 ILE D 2 LEU D 5 -1 N TYR D 4 O ILE D 11 SHEET 5 D 5 LYS D 65 MET D 67 1 O MET D 67 N GLY D 3 CISPEP 1 GLY B 125 ILE B 126 0 7.13 CISPEP 2 ILE B 126 ASP B 127 0 3.46 CISPEP 3 PRO D 124 GLY D 125 0 -3.49 CISPEP 4 GLY D 125 ILE D 126 0 5.08 CISPEP 5 ASP D 127 HIS D 128 0 -13.95 CRYST1 69.762 70.726 131.024 90.00 90.00 90.00 P 21 21 21 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 0.014334 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014139 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007632 0.00000