HEADER HYDROLASE 22-JAN-14 4OKK TITLE CRYSTAL STRUCTURE OF RNASE AS FROM M TUBERCULOSIS IN COMPLEX WITH UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3'-5' EXORIBONUCLEASE RV2179C/MT2234.1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RNASE AS; COMPND 5 EC: 3.1.13.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: RV2179C, MT2234.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA/BETA FOLD, EXORIBONUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ROMANO,R.VAN DE WEERD,F.C.C.BROUWER,G.N.ROVIELLO,R.LACROIX, AUTHOR 2 M.SPARRIUS,G.VAN DEN BRINK-VAN STEMPVOORT,J.J.MAASKANT,A.M.VAN DER AUTHOR 3 SAR,B.J.APPELMELK,J.J.GEURTSEN,R.BERISIO REVDAT 2 20-MAR-24 4OKK 1 REMARK SEQADV LINK REVDAT 1 21-MAY-14 4OKK 0 JRNL AUTH M.ROMANO,R.VAN DE WEERD,F.C.C.BROUWER,G.N.ROVIELLO, JRNL AUTH 2 R.LACROIX,M.SPARRIUS,G.VAN DEN BRINK-VAN STEMPVOORT, JRNL AUTH 3 J.J.MAASKANT,A.M.VAN DER SAR,B.J.APPELMELK,J.J.GEURTSEN, JRNL AUTH 4 R.BERISIO JRNL TITL STRUCTURE AND FUNCTION OF RNASE AS, A POLYADENYLATE-SPECIFIC JRNL TITL 2 EXORIBONUCLEASE AFFECTING MYCOBACTERIAL VIRULENCE IN VIVO JRNL REF STRUCTURE V. 22 719 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24704253 JRNL DOI 10.1016/J.STR.2014.01.014 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 15731 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 848 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) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1135 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2633 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 338 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 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): 0.379 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.262 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.239 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2761 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3770 ; 1.730 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 317 ; 6.734 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;30.528 ;21.806 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;16.420 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;19.415 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 402 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2168 ; 0.009 ; 0.021 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): 1603 ; 1.143 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2613 ; 2.071 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1158 ; 2.787 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1157 ; 4.537 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4OKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18023 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10%(W/V) POLYETHYLENE REMARK 280 GLYCOL 8000, 8%(V/V) ETHYLENE GLYCOL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 21.24450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.62200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.42400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.62200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.24450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.42400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 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 ASP A 161 REMARK 465 ALA A 162 REMARK 465 GLY A 163 REMARK 465 ARG A 164 REMARK 465 GLY A 165 REMARK 465 ALA A 166 REMARK 465 ALA A 167 REMARK 465 ARG A 168 REMARK 465 THR B 159 REMARK 465 ASP B 160 REMARK 465 ASP B 161 REMARK 465 ALA B 162 REMARK 465 GLY B 163 REMARK 465 ARG B 164 REMARK 465 GLY B 165 REMARK 465 ALA B 166 REMARK 465 ALA B 167 REMARK 465 ARG B 168 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 NH1 ARG A 121 OE2 GLU A 125 2.08 REMARK 500 NH1 ARG B 42 O HOH B 382 2.09 REMARK 500 OE1 GLU A 119 O HOH A 325 2.16 REMARK 500 O HOH A 323 O HOH A 336 2.16 REMARK 500 NE ARG B 127 O HOH B 419 2.17 REMARK 500 O HOH B 379 O HOH B 460 2.18 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 336 O HOH B 441 3655 2.12 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 HIS A 14 -56.28 -130.47 REMARK 500 HIS A 140 4.34 85.61 REMARK 500 HIS B 14 -56.06 -127.46 REMARK 500 PRO B 134 160.64 -46.82 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 HIS B 140 ASP B 141 149.54 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 121 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 U5P A 201 REMARK 610 U5P B 201 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 ASP A 6 OD1 REMARK 620 2 THR A 7 O 93.2 REMARK 620 3 ASP A 95 OD1 99.5 75.3 REMARK 620 4 U5P A 201 O2P 71.9 86.0 159.1 REMARK 620 5 HOH A 464 O 71.1 159.6 119.2 76.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 6 OD2 REMARK 620 2 ASP A 6 OD1 46.5 REMARK 620 3 GLU A 8 OE2 94.7 126.1 REMARK 620 4 U5P A 201 O2P 111.0 69.2 106.8 REMARK 620 5 HOH A 331 O 116.7 118.6 111.9 113.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 6 OD1 REMARK 620 2 U5P B 201 O2P 81.8 REMARK 620 3 U5P B 201 O3P 136.9 55.4 REMARK 620 4 HOH B 302 O 77.9 75.9 94.5 REMARK 620 5 HOH B 379 O 110.6 127.3 93.9 155.5 REMARK 620 6 HOH B 431 O 73.5 153.7 149.6 90.3 71.2 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 ASP B 6 OD2 REMARK 620 2 ASP B 6 OD1 48.1 REMARK 620 3 GLU B 8 OE2 91.6 125.8 REMARK 620 4 ASP B 145 OD2 109.9 127.0 97.0 REMARK 620 5 U5P B 201 O2P 124.2 85.6 94.8 124.1 REMARK 620 N 1 2 3 4 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 GLU B 37 OE2 REMARK 620 2 HOH B 387 O 112.9 REMARK 620 3 HOH B 402 O 88.6 126.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P 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 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OKE RELATED DB: PDB REMARK 900 RNASE AS IN COMPLEX WITH AMP REMARK 900 RELATED ID: 4OKJ RELATED DB: PDB REMARK 900 RNASE AS IN THE FREE STATE DBREF 4OKK A 2 168 UNP L7N5T0 EXRBN_MYCTU 2 168 DBREF 4OKK B 2 168 UNP L7N5T0 EXRBN_MYCTU 2 168 SEQADV 4OKK VAL A 1 UNP L7N5T0 EXPRESSION TAG SEQADV 4OKK VAL B 1 UNP L7N5T0 EXPRESSION TAG SEQRES 1 A 168 VAL ARG TYR PHE TYR ASP THR GLU PHE ILE GLU ASP GLY SEQRES 2 A 168 HIS THR ILE GLU LEU ILE SER ILE GLY VAL VAL ALA GLU SEQRES 3 A 168 ASP GLY ARG GLU TYR TYR ALA VAL SER THR GLU PHE ASP SEQRES 4 A 168 PRO GLU ARG ALA GLY SER TRP VAL ARG THR HIS VAL LEU SEQRES 5 A 168 PRO LYS LEU PRO PRO PRO ALA SER GLN LEU TRP ARG SER SEQRES 6 A 168 ARG GLN GLN ILE ARG LEU ASP LEU GLU GLU PHE LEU ARG SEQRES 7 A 168 ILE ASP GLY THR ASP SER ILE GLU LEU TRP ALA TRP VAL SEQRES 8 A 168 GLY ALA TYR ASP HIS VAL ALA LEU CYS GLN LEU TRP GLY SEQRES 9 A 168 PRO MET THR ALA LEU PRO PRO THR VAL PRO ARG PHE THR SEQRES 10 A 168 ARG GLU LEU ARG GLN LEU TRP GLU ASP ARG GLY CYS PRO SEQRES 11 A 168 ARG MET PRO PRO ARG PRO ARG ASP VAL HIS ASP ALA LEU SEQRES 12 A 168 VAL ASP ALA ARG ASP GLN LEU ARG ARG PHE ARG LEU ILE SEQRES 13 A 168 THR SER THR ASP ASP ALA GLY ARG GLY ALA ALA ARG SEQRES 1 B 168 VAL ARG TYR PHE TYR ASP THR GLU PHE ILE GLU ASP GLY SEQRES 2 B 168 HIS THR ILE GLU LEU ILE SER ILE GLY VAL VAL ALA GLU SEQRES 3 B 168 ASP GLY ARG GLU TYR TYR ALA VAL SER THR GLU PHE ASP SEQRES 4 B 168 PRO GLU ARG ALA GLY SER TRP VAL ARG THR HIS VAL LEU SEQRES 5 B 168 PRO LYS LEU PRO PRO PRO ALA SER GLN LEU TRP ARG SER SEQRES 6 B 168 ARG GLN GLN ILE ARG LEU ASP LEU GLU GLU PHE LEU ARG SEQRES 7 B 168 ILE ASP GLY THR ASP SER ILE GLU LEU TRP ALA TRP VAL SEQRES 8 B 168 GLY ALA TYR ASP HIS VAL ALA LEU CYS GLN LEU TRP GLY SEQRES 9 B 168 PRO MET THR ALA LEU PRO PRO THR VAL PRO ARG PHE THR SEQRES 10 B 168 ARG GLU LEU ARG GLN LEU TRP GLU ASP ARG GLY CYS PRO SEQRES 11 B 168 ARG MET PRO PRO ARG PRO ARG ASP VAL HIS ASP ALA LEU SEQRES 12 B 168 VAL ASP ALA ARG ASP GLN LEU ARG ARG PHE ARG LEU ILE SEQRES 13 B 168 THR SER THR ASP ASP ALA GLY ARG GLY ALA ALA ARG HET U5P A 201 20 HET MG A 202 1 HET MG A 203 1 HET MG A 204 1 HET U5P B 201 20 HET MG B 202 1 HET MG B 203 1 HET MG B 204 1 HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 4 MG 6(MG 2+) FORMUL 11 HOH *338(H2 O) HELIX 1 1 ASP A 39 ALA A 43 5 5 HELIX 2 2 GLY A 44 VAL A 51 1 8 HELIX 3 3 LEU A 52 LEU A 55 5 4 HELIX 4 4 SER A 65 LEU A 77 1 13 HELIX 5 5 GLY A 92 GLN A 101 1 10 HELIX 6 6 LEU A 102 GLY A 104 5 3 HELIX 7 7 PRO A 105 LEU A 109 5 5 HELIX 8 8 LEU A 120 ARG A 127 1 8 HELIX 9 9 ASP A 141 THR A 157 1 17 HELIX 10 10 ASP B 39 ALA B 43 5 5 HELIX 11 11 GLY B 44 VAL B 51 1 8 HELIX 12 12 LEU B 52 LEU B 55 5 4 HELIX 13 13 SER B 65 LEU B 77 1 13 HELIX 14 14 GLY B 92 GLN B 101 1 10 HELIX 15 15 PRO B 105 LEU B 109 5 5 HELIX 16 16 LEU B 120 ARG B 127 1 8 HELIX 17 17 ASP B 141 THR B 157 1 17 SHEET 1 A 6 TRP A 63 ARG A 64 0 SHEET 2 A 6 GLU A 30 SER A 35 1 N VAL A 34 O ARG A 64 SHEET 3 A 6 ILE A 16 ALA A 25 -1 N ILE A 19 O SER A 35 SHEET 4 A 6 ARG A 2 GLU A 11 -1 N PHE A 4 O VAL A 24 SHEET 5 A 6 GLU A 86 ALA A 89 1 O GLU A 86 N TYR A 3 SHEET 6 A 6 ARG A 118 GLU A 119 1 O ARG A 118 N LEU A 87 SHEET 1 B 6 TRP B 63 ARG B 64 0 SHEET 2 B 6 GLU B 30 SER B 35 1 N VAL B 34 O ARG B 64 SHEET 3 B 6 ILE B 16 ALA B 25 -1 N ILE B 19 O SER B 35 SHEET 4 B 6 ARG B 2 GLU B 11 -1 N ILE B 10 O GLU B 17 SHEET 5 B 6 GLU B 86 ALA B 89 1 O TRP B 88 N TYR B 5 SHEET 6 B 6 ARG B 118 GLU B 119 1 O ARG B 118 N LEU B 87 LINK O TYR A 5 MG MG A 203 1555 1555 2.86 LINK OD1 ASP A 6 MG MG A 202 1555 1555 2.46 LINK OD2 ASP A 6 MG MG A 204 1555 1555 1.97 LINK OD1 ASP A 6 MG MG A 204 1555 1555 3.00 LINK O THR A 7 MG MG A 202 1555 1555 2.79 LINK OE2 GLU A 8 MG MG A 204 1555 1555 1.86 LINK OD1 ASP A 95 MG MG A 202 1555 1555 2.67 LINK O2P U5P A 201 MG MG A 202 1555 1555 2.51 LINK O2P U5P A 201 MG MG A 204 1555 1555 1.86 LINK MG MG A 202 O HOH A 464 1555 1555 2.34 LINK MG MG A 204 O HOH A 331 1555 1555 1.94 LINK OD1 ASP B 6 MG MG B 202 1555 1555 2.33 LINK OD2 ASP B 6 MG MG B 204 1555 1555 1.80 LINK OD1 ASP B 6 MG MG B 204 1555 1555 2.96 LINK OE2 GLU B 8 MG MG B 204 1555 1555 1.99 LINK OE2 GLU B 37 MG MG B 203 1555 1555 2.55 LINK OD2 ASP B 145 MG MG B 204 1555 1555 1.88 LINK O2P U5P B 201 MG MG B 202 1555 1555 2.76 LINK O3P U5P B 201 MG MG B 202 1555 1555 2.90 LINK O2P U5P B 201 MG MG B 204 1555 1555 1.82 LINK MG MG B 202 O HOH B 302 1555 1555 2.32 LINK MG MG B 202 O HOH B 379 1555 1555 2.57 LINK MG MG B 202 O HOH B 431 1555 1555 2.44 LINK MG MG B 203 O HOH B 387 1555 1555 2.78 LINK MG MG B 203 O HOH B 402 1555 1555 2.88 SITE 1 AC1 10 ASP A 6 THR A 7 GLU A 8 PHE A 9 SITE 2 AC1 10 TRP A 46 VAL A 47 MG A 202 MG A 204 SITE 3 AC1 10 HOH A 346 HOH A 464 SITE 1 AC2 5 ASP A 6 THR A 7 ASP A 95 U5P A 201 SITE 2 AC2 5 HOH A 464 SITE 1 AC3 6 TYR A 5 ASP A 6 ALA A 89 TRP A 90 SITE 2 AC3 6 ASP A 145 GLN A 149 SITE 1 AC4 5 ASP A 6 GLU A 8 ASP A 145 U5P A 201 SITE 2 AC4 5 HOH A 331 SITE 1 AC5 11 MET A 106 ASP B 6 THR B 7 GLU B 8 SITE 2 AC5 11 PHE B 9 TRP B 46 VAL B 47 ASP B 145 SITE 3 AC5 11 MG B 202 MG B 204 HOH B 305 SITE 1 AC6 6 ASP B 6 U5P B 201 MG B 204 HOH B 302 SITE 2 AC6 6 HOH B 379 HOH B 431 SITE 1 AC7 6 GLU B 37 SER B 65 ARG B 66 GLN B 67 SITE 2 AC7 6 HOH B 387 HOH B 402 SITE 1 AC8 5 ASP B 6 GLU B 8 ASP B 145 U5P B 201 SITE 2 AC8 5 MG B 202 CRYST1 42.489 76.848 105.244 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 0.023536 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009502 0.00000