HEADER HYDROLASE/RNA/DNA 27-MAR-17 5VAJ TITLE BHRNASE H - AMIDE-RNA/DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*(URU)P*C)-3'); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RIBONUCLEASE H; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: RNASE H; COMPND 13 EC: 3.1.26.4; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 11 ORGANISM_TAXID: 272558; SOURCE 12 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 13 VARIANT: D132N; SOURCE 14 ATCC: 21591D; SOURCE 15 GENE: RNHA, BH0863; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: E COLI; SOURCE 19 EXPRESSION_SYSTEM_CELL: BL21; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS AMIDE-RNA, SIRNA, RNA X-RAY STRUCTURE, PHOSPHATE MODIFICATION, KEYWDS 2 RIBONUCLEASE H, AMIDE MODIFIED RNA-DNA., HYDROLASE-RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI REVDAT 3 04-OCT-23 5VAJ 1 LINK REVDAT 2 01-JAN-20 5VAJ 1 REMARK REVDAT 1 13-SEP-17 5VAJ 0 JRNL AUTH D.MUTISYA,T.HARDCASTLE,S.K.CHERUIYOT,P.S.PALLAN,S.D.KENNEDY, JRNL AUTH 2 M.EGLI,M.L.KELLEY,A.V.B.SMITH,E.ROZNERS JRNL TITL AMIDE LINKAGES MIMIC PHOSPHATES IN RNA INTERACTIONS WITH JRNL TITL 2 PROTEINS AND ARE WELL TOLERATED IN THE GUIDE STRAND OF SHORT JRNL TITL 3 INTERFERING RNAS. JRNL REF NUCLEIC ACIDS RES. V. 45 8142 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28854734 JRNL DOI 10.1093/NAR/GKX558 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28679 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1472 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2058 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2182 REMARK 3 NUCLEIC ACID ATOMS : 494 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.139 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.194 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2866 ; 0.018 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 2425 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3963 ; 1.380 ; 1.829 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5663 ; 1.905 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 7.301 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;35.340 ;24.906 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 419 ;16.024 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2753 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 560 ; 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): 1085 ; 2.258 ; 2.075 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1081 ; 2.223 ; 2.063 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1349 ; 3.258 ; 3.077 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1350 ; 3.262 ; 3.082 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1781 ; 3.014 ; 2.396 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1782 ; 3.013 ; 2.397 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2615 ; 4.664 ; 3.455 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3443 ; 6.585 ;23.822 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3408 ; 6.483 ;23.588 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 5VAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000227115. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 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: 1ZBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE (PH 6.5) AND REMARK 280 0.7 M SODIUM ACETATE., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.59000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.75650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.59000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.75650 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: 7680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 GLY A 55 REMARK 465 SER A 56 REMARK 465 HIS A 57 REMARK 465 MET A 58 REMARK 465 ALA A 59 REMARK 465 LYS A 60 REMARK 465 GLU A 61 REMARK 465 GLY B 55 REMARK 465 SER B 56 REMARK 465 HIS B 57 REMARK 465 MET B 58 REMARK 465 ARG B 195 REMARK 465 LYS B 196 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 VAL A 72 CG1 REMARK 470 GLU A 175 CG CD OE1 OE2 REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 196 CB CG CD CE NZ REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 GLU B 175 CG CD OE1 OE2 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 B 351 O HOH B 363 2.00 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 C C 6 O5' - P - OP2 ANGL. DEV. = -6.9 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 GLU B 98 138.59 -36.31 REMARK 500 LYS B 146 59.96 -108.74 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 A 388 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 389 DISTANCE = 5.98 ANGSTROMS 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 B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 5 OP1 REMARK 620 2 ASP B 71 OD1 80.2 REMARK 620 3 GLU B 109 OE1 155.6 96.0 REMARK 620 4 GLU B 109 OE2 112.5 119.0 48.5 REMARK 620 5 ASN B 132 OD1 100.9 144.8 95.9 93.3 REMARK 620 6 HOH B 326 O 138.8 88.5 64.5 107.6 67.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 5 OP1 REMARK 620 2 ASP B 71 OD2 101.4 REMARK 620 3 ASP B 192 OD1 155.3 97.3 REMARK 620 4 HOH B 310 O 111.8 92.5 83.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 206 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 URU C 10 OP1 REMARK 620 2 ASP A 71 OD1 71.9 REMARK 620 3 GLU A 109 OE1 147.8 96.4 REMARK 620 4 GLU A 109 OE2 108.2 116.8 49.5 REMARK 620 5 ASN A 132 OD1 103.4 139.6 104.4 102.9 REMARK 620 6 HOH A 336 O 139.7 86.1 65.7 111.8 72.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 207 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 URU C 10 OP1 REMARK 620 2 ASP A 71 OD2 102.4 REMARK 620 3 ASP A 192 OD1 158.5 98.6 REMARK 620 4 HOH A 334 O 106.3 87.8 78.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 206 DBREF 5VAJ C 1 12 PDB 5VAJ 5VAJ 1 12 DBREF 5VAJ D 1 12 PDB 5VAJ 5VAJ 1 12 DBREF 5VAJ A 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 DBREF 5VAJ B 59 196 UNP Q9KEI9 RNH1_BACHD 59 196 SEQADV 5VAJ GLY A 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ SER A 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ HIS A 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ MET A 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ ASN A 132 UNP Q9KEI9 ASP 132 CONFLICT SEQADV 5VAJ GLY B 55 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ SER B 56 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ HIS B 57 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ MET B 58 UNP Q9KEI9 EXPRESSION TAG SEQADV 5VAJ ASN B 132 UNP Q9KEI9 ASP 132 CONFLICT SEQRES 1 C 11 G A C A C C U G A URU C SEQRES 1 D 12 DG DA DA DT DC DA DG DG DT DG DT DC SEQRES 1 A 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 A 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 A 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 A 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 A 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 A 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASN SEQRES 7 A 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 A 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 A 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 A 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 A 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS SEQRES 1 B 142 GLY SER HIS MET ALA LYS GLU GLU ILE ILE TRP GLU SER SEQRES 2 B 142 LEU SER VAL ASP VAL GLY SER GLN GLY ASN PRO GLY ILE SEQRES 3 B 142 VAL GLU TYR LYS GLY VAL ASP THR LYS THR GLY GLU VAL SEQRES 4 B 142 LEU PHE GLU ARG GLU PRO ILE PRO ILE GLY THR ASN ASN SEQRES 5 B 142 MET GLY GLU PHE LEU ALA ILE VAL HIS GLY LEU ARG TYR SEQRES 6 B 142 LEU LYS GLU ARG ASN SER ARG LYS PRO ILE TYR SER ASN SEQRES 7 B 142 SER GLN THR ALA ILE LYS TRP VAL LYS ASP LYS LYS ALA SEQRES 8 B 142 LYS SER THR LEU VAL ARG ASN GLU GLU THR ALA LEU ILE SEQRES 9 B 142 TRP LYS LEU VAL ASP GLU ALA GLU GLU TRP LEU ASN THR SEQRES 10 B 142 HIS THR TYR GLU THR PRO ILE LEU LYS TRP GLN THR ASP SEQRES 11 B 142 LYS TRP GLY GLU ILE LYS ALA ASP TYR GLY ARG LYS HET URU C 10 39 HET GOL C 101 6 HET GOL D 101 6 HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET GOL A 205 6 HET MG A 206 1 HET MG A 207 1 HET ACT A 208 4 HET GOL B 201 6 HET GOL B 202 6 HET MG B 203 1 HET MG B 204 1 HET ACT B 205 4 HET ACT B 206 4 HETNAM URU ((2S,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)- HETNAM 2 URU YL)-3-(2- ((((2R,5R)-5-(2,4-DIOXO-3,4- HETNAM 3 URU DIHYDROPYRIMIDIN-1(2H)-YL)- 3,4- HETNAM 4 URU DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL)AMINO)-2- HETNAM 5 URU OXOETHYL)-4- HYDROXYTETRAHYDROFURAN-2-YL)METHYL HETNAM 6 URU PHOSPHATE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 URU C20 H26 N5 O14 P FORMUL 5 GOL 9(C3 H8 O3) FORMUL 12 MG 4(MG 2+) FORMUL 14 ACT 3(C2 H3 O2 1-) FORMUL 21 HOH *214(H2 O) HELIX 1 AA1 THR A 104 ARG A 123 1 20 HELIX 2 AA2 SER A 133 LYS A 143 1 11 HELIX 3 AA3 ASN A 152 GLU A 154 5 3 HELIX 4 AA4 THR A 155 ASN A 170 1 16 HELIX 5 AA5 GLN A 182 GLY A 187 1 6 HELIX 6 AA6 THR B 104 ARG B 123 1 20 HELIX 7 AA7 SER B 133 LYS B 143 1 11 HELIX 8 AA8 THR B 155 THR B 171 1 17 HELIX 9 AA9 GLN B 182 GLY B 187 1 6 SHEET 1 AA1 3 VAL A 93 GLU A 96 0 SHEET 2 AA1 3 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA1 3 ILE A 100 GLY A 103 -1 O ILE A 100 N VAL A 81 SHEET 1 AA2 5 VAL A 93 GLU A 96 0 SHEET 2 AA2 5 GLY A 79 ASP A 87 -1 N GLY A 85 O LEU A 94 SHEET 3 AA2 5 LEU A 68 GLN A 75 -1 N SER A 69 O VAL A 86 SHEET 4 AA2 5 ILE A 129 SER A 131 1 O TYR A 130 N LEU A 68 SHEET 5 AA2 5 ILE A 178 LYS A 180 1 O LEU A 179 N ILE A 129 SHEET 1 AA3 5 VAL B 93 GLY B 103 0 SHEET 2 AA3 5 GLY B 79 ASP B 87 -1 N VAL B 81 O ILE B 100 SHEET 3 AA3 5 LEU B 68 GLN B 75 -1 N GLY B 73 O GLU B 82 SHEET 4 AA3 5 ILE B 129 SER B 131 1 O TYR B 130 N LEU B 68 SHEET 5 AA3 5 ILE B 178 LYS B 180 1 O LEU B 179 N ILE B 129 LINK O3' A C 9 P URU C 10 1555 1555 1.61 LINK OX' URU C 10 P C C 12 1555 1555 1.65 LINK OP1 C C 5 MG MG B 203 1555 1555 2.66 LINK OP1 C C 5 MG MG B 204 1555 1555 2.25 LINK OP1 URU C 10 MG MG A 206 1555 1555 2.75 LINK OP1 URU C 10 MG MG A 207 1555 1555 2.12 LINK OD1 ASP A 71 MG MG A 206 1555 1555 2.19 LINK OD2 ASP A 71 MG MG A 207 1555 1555 2.14 LINK OE1 GLU A 109 MG MG A 206 1555 1555 2.80 LINK OE2 GLU A 109 MG MG A 206 1555 1555 2.34 LINK OD1 ASN A 132 MG MG A 206 1555 1555 2.18 LINK OD1 ASP A 192 MG MG A 207 1555 1555 2.36 LINK MG MG A 206 O HOH A 336 1555 1555 2.73 LINK MG MG A 207 O HOH A 334 1555 1555 2.28 LINK OD1 ASP B 71 MG MG B 203 1555 1555 2.02 LINK OD2 ASP B 71 MG MG B 204 1555 1555 2.23 LINK OE1 GLU B 109 MG MG B 203 1555 1555 2.97 LINK OE2 GLU B 109 MG MG B 203 1555 1555 2.29 LINK OD1 ASN B 132 MG MG B 203 1555 1555 2.50 LINK OD1 ASP B 192 MG MG B 204 1555 1555 2.21 LINK MG MG B 203 O HOH B 326 1555 1555 2.84 LINK MG MG B 204 O HOH B 310 1555 1555 2.37 CISPEP 1 ASN A 77 PRO A 78 0 0.18 CISPEP 2 ASN B 77 PRO B 78 0 2.37 SITE 1 AC1 3 G C 8 A C 9 HOH C 203 SITE 1 AC2 3 DG D 7 DG D 8 DT D 9 SITE 1 AC3 6 ASN A 152 ALA A 156 HOH A 342 GLU B 62 SITE 2 AC3 6 ILE B 63 TRP B 65 SITE 1 AC4 7 TYR A 83 LEU A 111 HIS A 115 ARG A 118 SITE 2 AC4 7 GLU A 164 ALA A 165 HOH A 319 SITE 1 AC5 7 HIS A 115 ARG A 118 TYR A 119 ARG A 123 SITE 2 AC5 7 GLU A 167 ASN A 170 HOH A 301 SITE 1 AC6 5 GLY A 73 SER A 74 GLN A 75 GLU A 82 SITE 2 AC6 5 HOH A 353 SITE 1 AC7 4 LYS A 143 HIS A 172 THR A 173 TYR A 174 SITE 1 AC8 6 ASP A 71 GLU A 109 ASN A 132 HOH A 336 SITE 2 AC8 6 A C 9 URU C 10 SITE 1 AC9 4 ASP A 71 ASP A 192 HOH A 334 URU C 10 SITE 1 AD1 3 GLY A 76 ASN A 77 PRO A 78 SITE 1 AD2 6 TYR B 83 ARG B 97 HIS B 115 ARG B 118 SITE 2 AD2 6 GLU B 164 HOH B 308 SITE 1 AD3 7 VAL B 93 GLU B 96 ARG B 118 GLU B 164 SITE 2 AD3 7 TRP B 168 HIS B 172 HOH B 325 SITE 1 AD4 6 ASP B 71 GLU B 109 ASN B 132 HOH B 326 SITE 2 AD4 6 A C 4 C C 5 SITE 1 AD5 4 ASP B 71 ASP B 192 HOH B 310 C C 5 SITE 1 AD6 5 GLU B 122 ARG B 123 ARG B 151 ASP B 163 SITE 2 AD6 5 HOH B 353 SITE 1 AD7 2 GLU B 167 HOH B 333 CRYST1 137.180 37.513 93.863 90.00 121.65 90.00 C 1 2 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 0.007290 0.000000 0.004494 0.00000 SCALE2 0.000000 0.026657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012516 0.00000