HEADER LIGASE 20-JUL-15 5COT TITLE STRUCTURE AND MECHANISM OF A EUKARYAL NICK-SEALING RNA LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAEGLERIA GRUBERI RNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAEGLERIA GRUBERI; SOURCE 3 ORGANISM_COMMON: AMOEBA; SOURCE 4 ORGANISM_TAXID: 5762; SOURCE 5 GENE: NAEGRDRAFT_82186; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA REPAIR, ADENYLYLTRANSFERASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN REVDAT 5 25-DEC-19 5COT 1 REMARK REVDAT 4 06-SEP-17 5COT 1 JRNL REMARK REVDAT 3 25-NOV-15 5COT 1 JRNL REVDAT 2 11-NOV-15 5COT 1 JRNL REVDAT 1 28-OCT-15 5COT 0 JRNL AUTH M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN JRNL TITL STRUCTURE AND TWO-METAL MECHANISM OF A EUKARYAL NICK-SEALING JRNL TITL 2 RNA LIGASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 13868 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26512110 JRNL DOI 10.1073/PNAS.1516536112 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0124 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36965 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1950 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2683 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2717 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.265 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2788 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2685 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3757 ; 2.183 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6179 ; 1.197 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 6.595 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;35.624 ;24.643 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;15.658 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.756 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3163 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 645 ; 0.002 ; 0.020 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): 1359 ; 2.357 ; 2.409 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1358 ; 2.357 ; 2.409 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1697 ; 3.064 ; 3.607 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1698 ; 3.063 ; 3.607 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1429 ; 3.736 ; 2.752 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1430 ; 3.735 ; 2.751 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2061 ; 5.419 ; 3.967 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3655 ; 7.278 ;21.672 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3338 ; 6.966 ;20.195 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5COT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 30% PEG 6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.36333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.18167 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HOH A 554 O HOH A 571 1.12 REMARK 500 O HOH A 529 O HOH A 637 1.27 REMARK 500 O HOH A 605 O HOH A 695 1.32 REMARK 500 O HOH A 622 O HOH A 820 1.37 REMARK 500 O HOH A 797 O HOH A 827 1.52 REMARK 500 O HOH A 539 O HOH A 921 1.59 REMARK 500 O HOH A 501 O HOH A 909 1.67 REMARK 500 O ARG A 87 O HOH A 501 1.74 REMARK 500 O HOH A 502 O HOH A 873 1.74 REMARK 500 O HOH A 667 O HOH A 861 1.81 REMARK 500 O HOH A 518 O HOH A 638 1.81 REMARK 500 O HOH A 704 O HOH A 921 1.83 REMARK 500 O HOH A 676 O HOH A 758 1.86 REMARK 500 O HOH A 663 O HOH A 873 1.87 REMARK 500 O HOH A 695 O HOH A 802 2.03 REMARK 500 O HOH A 818 O HOH A 946 2.03 REMARK 500 UNK UNX A 402 O HOH A 645 2.07 REMARK 500 O HOH A 506 O HOH A 633 2.07 REMARK 500 NH1 ARG A 82 O HOH A 502 2.08 REMARK 500 O1P AMP A 401 UNK UNX A 402 2.10 REMARK 500 UNK UNX A 402 O HOH A 511 2.14 REMARK 500 O HOH A 510 O HOH A 946 2.14 REMARK 500 O HOH A 576 O HOH A 924 2.14 REMARK 500 O HOH A 507 O HOH A 940 2.17 REMARK 500 UNK UNX A 402 O HOH A 514 2.18 REMARK 500 UNK UNX A 402 O HOH A 565 2.19 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 O HOH A 607 O HOH A 767 3465 2.15 REMARK 500 O HOH A 609 O HOH A 853 3565 2.17 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 THR A 33 CB THR A 33 CG2 -0.200 REMARK 500 CYS A 34 CA CYS A 34 CB 0.133 REMARK 500 CYS A 34 CB CYS A 34 SG -0.155 REMARK 500 GLU A 115 CD GLU A 115 OE1 0.084 REMARK 500 THR A 199 CB THR A 199 CG2 -0.210 REMARK 500 GLU A 294 CG GLU A 294 CD 0.096 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 LYS A 38 CD - CE - NZ ANGL. DEV. = -17.1 DEGREES REMARK 500 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 172 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 286 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 LEU A 319 CB - CG - CD1 ANGL. DEV. = 12.3 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 ASP A 30 -129.49 47.35 REMARK 500 ASP A 53 -6.93 83.80 REMARK 500 ASP A 59 105.13 -168.84 REMARK 500 ASP A 182 -124.68 51.81 REMARK 500 ASN A 290 59.47 -162.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1024 DISTANCE = 5.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AMP A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5COU RELATED DB: PDB REMARK 900 RELATED ID: 5COV RELATED DB: PDB DBREF 5COT A 1 339 UNP D2W2Z5 D2W2Z5_NAEGR 1 339 SEQADV 5COT SER A 0 UNP D2W2Z5 EXPRESSION TAG SEQRES 1 A 340 SER MET GLY VAL ARG LYS LEU ALA THR ILE ARG THR ALA SEQRES 2 A 340 GLY GLU ILE THR PRO ILE ALA GLY ALA GLU ALA ILE GLU SEQRES 3 A 340 CYS CYS HIS VAL ASP GLY TRP THR CYS VAL ILE LYS LYS SEQRES 4 A 340 GLY GLU PHE LYS GLN GLY ASP ARG GLY VAL TYR PHE GLU SEQRES 5 A 340 ILE ASP SER PHE ILE LYS GLU ASP ASN ASP ARG TYR PRO SEQRES 6 A 340 MET LEU SER LYS GLN VAL ILE ASP TYR GLU GLY GLN ARG SEQRES 7 A 340 GLY THR ARG LEU ARG THR ALA ARG LEU ARG GLY GLN LEU SEQRES 8 A 340 SER GLN GLY LEU PHE LEU PRO MET ASP ARG PHE PRO GLU SEQRES 9 A 340 LEU ALA SER ASN GLN VAL GLY ASP ASP VAL THR GLU ILE SEQRES 10 A 340 LEU GLY ILE THR LYS TRP GLU PRO PRO ILE SER THR ASN SEQRES 11 A 340 LEU SER GLY GLU ILE LEU GLY GLU PHE PRO THR PHE ILE SEQRES 12 A 340 SER LYS THR ASP GLN GLU ARG VAL GLN ASN LEU ILE PRO SEQRES 13 A 340 GLN ILE GLU GLU ASN LYS GLY GLN LYS PHE GLU VAL THR SEQRES 14 A 340 VAL LYS LEU ASP GLY SER SER MET THR VAL TYR ARG LYS SEQRES 15 A 340 ASP ASP HIS ILE GLY VAL CYS GLY ARG ASN TRP GLU LEU SEQRES 16 A 340 ARG GLU THR ALA THR ASN ALA GLN TRP HIS ALA ALA ARG SEQRES 17 A 340 ARG ASN LYS MET ILE GLU GLY LEU GLN PHE LEU ASN ARG SEQRES 18 A 340 ASN LEU ALA LEU GLN GLY GLU ILE ILE GLY GLU SER ILE SEQRES 19 A 340 GLN GLY ASN LEU GLU LYS LEU LYS GLY GLN ASP PHE TYR SEQRES 20 A 340 LEU PHE ASP ILE TYR ASP ILE ASP LYS ALA GLN TYR LEU SEQRES 21 A 340 THR PRO ILE GLU ARG GLN SER LEU VAL LYS GLN LEU ASN SEQRES 22 A 340 ASP ASN GLY PHE THR VAL LYS HIS VAL PRO ILE LEU ASP SEQRES 23 A 340 ASP LEU GLU LEU ASN HIS THR ALA GLU GLN ILE LEU ALA SEQRES 24 A 340 MET ALA ASP GLY PRO SER LEU ASN LYS ASN VAL LYS ARG SEQRES 25 A 340 GLU GLY LEU VAL PHE LYS ARG LEU ASP GLY LYS PHE SER SEQRES 26 A 340 PHE LYS ALA ILE SER ASN ALA TYR LEU GLU LYS HIS LYS SEQRES 27 A 340 ASP ARG HET AMP A 401 22 HET UNX A 402 1 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 UNX X FORMUL 4 HOH *524(H2 O) HELIX 1 AA1 TYR A 63 VAL A 70 5 8 HELIX 2 AA2 ASP A 99 ALA A 105 5 7 HELIX 3 AA3 VAL A 113 GLY A 118 1 6 HELIX 4 AA4 SER A 127 SER A 131 5 5 HELIX 5 AA5 ARG A 149 ASN A 152 5 4 HELIX 6 AA6 LEU A 153 ASN A 160 1 8 HELIX 7 AA7 ASN A 200 ASN A 209 1 10 HELIX 8 AA8 LYS A 210 ASN A 219 1 10 HELIX 9 AA9 THR A 260 ASN A 274 1 15 HELIX 10 AB1 THR A 292 ALA A 300 1 9 HELIX 11 AB2 SER A 329 HIS A 336 1 8 SHEET 1 AA1 5 TRP A 32 LYS A 37 0 SHEET 2 AA1 5 ILE A 24 VAL A 29 -1 N GLU A 25 O ILE A 36 SHEET 3 AA1 5 ALA A 7 PRO A 17 -1 N GLY A 13 O HIS A 28 SHEET 4 AA1 5 ARG A 46 PHE A 50 -1 O TYR A 49 N THR A 8 SHEET 5 AA1 5 LEU A 94 PRO A 97 -1 O LEU A 94 N PHE A 50 SHEET 1 AA2 4 ILE A 71 TYR A 73 0 SHEET 2 AA2 4 GLN A 76 ARG A 80 -1 O GLY A 78 N ILE A 71 SHEET 3 AA2 4 SER A 54 LYS A 57 -1 N ILE A 56 O THR A 79 SHEET 4 AA2 4 THR A 120 LYS A 121 -1 O THR A 120 N PHE A 55 SHEET 1 AA3 2 ALA A 84 LEU A 86 0 SHEET 2 AA3 2 GLN A 89 SER A 91 -1 O GLN A 89 N LEU A 86 SHEET 1 AA4 7 ILE A 134 GLU A 137 0 SHEET 2 AA4 7 TRP A 192 LEU A 194 -1 O GLU A 193 N LEU A 135 SHEET 3 AA4 7 HIS A 184 CYS A 188 -1 N VAL A 187 O LEU A 194 SHEET 4 AA4 7 SER A 174 LYS A 181 -1 N THR A 177 O CYS A 188 SHEET 5 AA4 7 LEU A 222 GLY A 230 -1 O LEU A 224 N VAL A 178 SHEET 6 AA4 7 GLN A 243 ASP A 252 -1 O ASP A 249 N GLN A 225 SHEET 7 AA4 7 GLN A 257 TYR A 258 -1 O GLN A 257 N ASP A 252 SHEET 1 AA5 7 ILE A 134 GLU A 137 0 SHEET 2 AA5 7 TRP A 192 LEU A 194 -1 O GLU A 193 N LEU A 135 SHEET 3 AA5 7 HIS A 184 CYS A 188 -1 N VAL A 187 O LEU A 194 SHEET 4 AA5 7 SER A 174 LYS A 181 -1 N THR A 177 O CYS A 188 SHEET 5 AA5 7 LEU A 222 GLY A 230 -1 O LEU A 224 N VAL A 178 SHEET 6 AA5 7 GLN A 243 ASP A 252 -1 O ASP A 249 N GLN A 225 SHEET 7 AA5 7 LYS A 279 HIS A 280 1 O LYS A 279 N LEU A 247 SHEET 1 AA6 4 LEU A 287 GLU A 288 0 SHEET 2 AA6 4 LYS A 164 LYS A 170 -1 N PHE A 165 O LEU A 287 SHEET 3 AA6 4 GLY A 313 ARG A 318 -1 O LYS A 317 N GLU A 166 SHEET 4 AA6 4 SER A 324 ILE A 328 -1 O PHE A 325 N PHE A 316 LINK NZ LYS A 170 P AMP A 401 1555 1555 1.75 SITE 1 AC1 19 THR A 145 THR A 168 VAL A 169 LYS A 170 SITE 2 AC1 19 LEU A 171 SER A 175 GLU A 227 PHE A 248 SITE 3 AC1 19 VAL A 281 VAL A 315 LYS A 317 LYS A 326 SITE 4 AC1 19 ILE A 328 HOH A 511 HOH A 561 HOH A 563 SITE 5 AC1 19 HOH A 591 HOH A 828 HOH A 842 CRYST1 55.285 55.285 102.545 90.00 90.00 120.00 P 32 3 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 0.018088 0.010443 0.000000 0.00000 SCALE2 0.000000 0.020886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009752 0.00000