HEADER LIGASE 06-NOV-14 4RR8 TITLE N-TERMINAL EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM AEROPYRUM TITLE 2 PERNIX WITH L-SER3AA (SNAPSHOT 3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE THREONINE--TRNA LIGASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-136; COMPND 5 SYNONYM: THREONYL-TRNA SYNTHETASE 2, THRRS 2; COMPND 6 EC: 6.1.1.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX K1; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1; SOURCE 5 GENE: THRS2, APE_0117.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DTD-LIKE FOLD, PROOFREADING, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.AHMAD,S.MUTHUKUMAR,A.S.K.YERABHAM,V.KAMARTHAPU,R.SANKARANARAYANAN REVDAT 2 22-NOV-17 4RR8 1 REMARK REVDAT 1 15-JUL-15 4RR8 0 JRNL AUTH S.AHMAD,S.MUTHUKUMAR,S.K.KUNCHA,S.B.ROUTH,A.S.YERABHAM, JRNL AUTH 2 T.HUSSAIN,V.KAMARTHAPU,S.P.KRUPARANI,R.SANKARANARAYANAN JRNL TITL SPECIFICITY AND CATALYSIS HARDWIRED AT THE RNA-PROTEIN JRNL TITL 2 INTERFACE IN A TRANSLATIONAL PROOFREADING ENZYME. JRNL REF NAT COMMUN V. 6 7552 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26113036 JRNL DOI 10.1038/NCOMMS8552 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11182 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 556 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1068 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : -1.21000 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): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.218 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1101 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1502 ; 1.633 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 135 ; 6.971 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 40 ;42.874 ;22.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;14.351 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;12.120 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 167 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 834 ; 0.009 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4RR8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 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) : 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 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, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.2M MGCL2, 30% PEG4000, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 57.17300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.91200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.91200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.58650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.91200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.91200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 85.75950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.91200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.91200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.58650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.91200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.91200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 85.75950 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 57.17300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 57.17300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 424 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 49 CD OE1 NE2 REMARK 480 ARG A 64 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 66 CD CE NZ REMARK 480 ARG A 81 CD NE CZ NH1 NH2 REMARK 480 LYS A 84 CE NZ REMARK 480 LYS A 90 CG CD CE NZ REMARK 480 ARG A 91 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 O LYS A 123 O HOH A 305 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 49 CG GLN A 49 CD -0.198 REMARK 500 ARG A 81 CG ARG A 81 CD -0.166 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 ARG A 91 NE - CZ - NH1 ANGL. DEV. = -21.1 DEGREES REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = 15.9 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 VAL A 16 -112.75 -126.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 91 0.23 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 324 O REMARK 620 2 HOH A 351 O 95.1 REMARK 620 3 HOH A 401 O 99.1 165.7 REMARK 620 4 HOH A 380 O 171.0 77.5 88.3 REMARK 620 5 HOH A 366 O 88.1 79.0 101.6 85.3 REMARK 620 6 HOH A 374 O 93.7 94.2 84.7 92.1 173.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A3S A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RR6 RELATED DB: PDB REMARK 900 RELATED ID: 4RR7 RELATED DB: PDB REMARK 900 RELATED ID: 4RR9 RELATED DB: PDB REMARK 900 RELATED ID: 4RRA RELATED DB: PDB REMARK 900 RELATED ID: 4RRB RELATED DB: PDB REMARK 900 RELATED ID: 4RRC RELATED DB: PDB REMARK 900 RELATED ID: 4RRD RELATED DB: PDB REMARK 900 RELATED ID: 4RRF RELATED DB: PDB REMARK 900 RELATED ID: 4RRG RELATED DB: PDB REMARK 900 RELATED ID: 4RRH RELATED DB: PDB REMARK 900 RELATED ID: 4RRI RELATED DB: PDB REMARK 900 RELATED ID: 4RRJ RELATED DB: PDB REMARK 900 RELATED ID: 4RRK RELATED DB: PDB REMARK 900 RELATED ID: 4RRL RELATED DB: PDB REMARK 900 RELATED ID: 4RRM RELATED DB: PDB REMARK 900 RELATED ID: 4RRQ RELATED DB: PDB REMARK 900 RELATED ID: 4RRR RELATED DB: PDB DBREF 4RR8 A 1 136 UNP Q9YFY3 SYT2_AERPE 1 136 SEQRES 1 A 136 MET ARG LEU LEU TYR LEU HIS ALA ASP ARG PHE GLU TYR SEQRES 2 A 136 LYS THR VAL LYS PRO ALA LEU LYS ASN PRO PRO ASP PRO SEQRES 3 A 136 PRO GLY GLU ALA SER PHE GLY GLU ALA LEU VAL VAL PHE SEQRES 4 A 136 THR THR VAL GLU ASP GLY ASP GLY PRO GLN THR VAL MET SEQRES 5 A 136 TYR ALA ALA SER ASP ILE ALA SER HIS SER SER ARG LEU SEQRES 6 A 136 LYS VAL THR THR VAL ILE LEU TYR PRO TYR ALA HIS LEU SEQRES 7 A 136 SER SER ARG LEU ALA LYS PRO MET ALA ALA HIS LYS ARG SEQRES 8 A 136 LEU ILE GLU LEU GLU GLY ALA LEU ARG THR LYS PHE PRO SEQRES 9 A 136 GLY HIS VAL HIS ARG ALA PRO PHE GLY TRP TYR LYS SER SEQRES 10 A 136 PHE SER ILE ALA CYS LYS GLY HIS PRO LEU ALA GLU LEU SEQRES 11 A 136 SER ARG SER PHE THR GLU HET A3S A 201 25 HET MG A 202 1 HETNAM A3S SERINE-3'-AMINOADENOSINE HETNAM MG MAGNESIUM ION HETSYN A3S N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE FORMUL 2 A3S C13 H19 N7 O5 FORMUL 3 MG MG 2+ FORMUL 4 HOH *169(H2 O) HELIX 1 1 GLY A 47 LYS A 66 1 20 HELIX 2 2 LYS A 84 THR A 101 1 18 SHEET 1 A 3 GLU A 29 PHE A 32 0 SHEET 2 A 3 ARG A 2 PRO A 18 -1 N PHE A 11 O PHE A 32 SHEET 3 A 3 TRP A 114 CYS A 122 -1 O TYR A 115 N LYS A 17 SHEET 1 B 5 HIS A 106 ARG A 109 0 SHEET 2 B 5 THR A 69 PRO A 74 1 N LEU A 72 O HIS A 108 SHEET 3 B 5 ALA A 35 THR A 41 1 N VAL A 38 O ILE A 71 SHEET 4 B 5 ARG A 2 PRO A 18 -1 N LEU A 6 O VAL A 37 SHEET 5 B 5 GLU A 129 SER A 133 -1 O LEU A 130 N TYR A 5 LINK MG MG A 202 O HOH A 324 1555 1555 2.06 LINK MG MG A 202 O HOH A 351 1555 1555 2.21 LINK MG MG A 202 O HOH A 401 1555 1555 2.26 LINK MG MG A 202 O HOH A 380 1555 1555 2.32 LINK MG MG A 202 O HOH A 366 1555 1555 2.34 LINK MG MG A 202 O HOH A 374 1555 1555 2.35 SITE 1 AC1 24 ALA A 19 THR A 40 VAL A 42 PRO A 74 SITE 2 AC1 24 TYR A 75 ALA A 76 HIS A 77 LEU A 82 SITE 3 AC1 24 ALA A 83 ALA A 88 PHE A 112 GLY A 113 SITE 4 AC1 24 TRP A 114 TYR A 115 LYS A 116 GLU A 129 SITE 5 AC1 24 HOH A 319 HOH A 321 HOH A 323 HOH A 408 SITE 6 AC1 24 HOH A 409 HOH A 410 HOH A 441 HOH A 464 SITE 1 AC2 6 HOH A 324 HOH A 351 HOH A 366 HOH A 374 SITE 2 AC2 6 HOH A 380 HOH A 401 CRYST1 47.824 47.824 114.346 90.00 90.00 90.00 P 41 21 2 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 0.020910 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008745 0.00000 MASTER 406 0 2 2 8 0 8 6 0 0 0 11 END