HEADER ENDORIBONUCLEASE 11-SEP-98 1BU4 TITLE RIBONUCLEASE 1 COMPLEX WITH 2'GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE T1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.27.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS ORYZAE; SOURCE 3 ORGANISM_TAXID: 5062; SOURCE 4 GENE: SYNTHETIC GENE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PMC5-RT1; SOURCE 8 EXPRESSION_SYSTEM_GENE: SYNTHETIC GENE KEYWDS HYDROLASE, ENDORIBONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR R.LORIS,S.DEVOS,U.LANGHORST,K.DECANNIERE,J.BOUCKAERT,D.MAES, AUTHOR 2 T.R.TRANSUE,J.STEYAERT REVDAT 4 03-APR-24 1BU4 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1BU4 1 VERSN REVDAT 2 01-APR-03 1BU4 1 JRNL REVDAT 1 16-FEB-99 1BU4 0 JRNL AUTH R.LORIS,U.LANGHORST,S.DE VOS,K.DECANNIERE,J.BOUCKAERT, JRNL AUTH 2 D.MAES,T.R.TRANSUE,J.STEYAERT JRNL TITL CONSERVED WATER MOLECULES IN A LARGE FAMILY OF MICROBIAL JRNL TITL 2 RIBONUCLEASES. JRNL REF PROTEINS V. 36 117 1999 JRNL REFN ISSN 0887-3585 JRNL PMID 10373011 JRNL DOI 10.1002/(SICI)1097-0134(19990701)36:1<117::AID-PROT10>3.0.CO JRNL DOI 2 ;2-H REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 7907 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 771 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 781 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-98 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 95.6 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13900 REMARK 200 FOR THE DATA SET : 12.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58300 REMARK 200 FOR SHELL : 2.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.5 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 20.25500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.40500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.40500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.25500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.00000 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: MONOMERIC 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 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 ASP A 15 OD2 46.8 REMARK 620 3 HOH A 216 O 78.7 74.4 REMARK 620 4 HOH A 221 O 124.6 77.9 92.7 REMARK 620 5 HOH A 225 O 74.5 121.3 95.5 160.5 REMARK 620 6 HOH A 236 O 78.6 78.0 151.9 86.5 94.3 REMARK 620 7 HOH A 241 O 146.6 137.7 74.0 76.2 89.2 132.5 REMARK 620 8 HOH A 291 O 135.4 127.5 145.7 70.7 92.9 59.5 73.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: CAL REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CALCIUM BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GP A 202 DBREF 1BU4 A 1 104 UNP P00651 RNT1_ASPOR 27 130 SEQADV 1BU4 LYS A 25 UNP P00651 GLN 51 CONFLICT SEQRES 1 A 104 ALA CYS ASP TYR THR CYS GLY SER ASN CYS TYR SER SER SEQRES 2 A 104 SER ASP VAL SER THR ALA GLN ALA ALA GLY TYR LYS LEU SEQRES 3 A 104 HIS GLU ASP GLY GLU THR VAL GLY SER ASN SER TYR PRO SEQRES 4 A 104 HIS LYS TYR ASN ASN TYR GLU GLY PHE ASP PHE SER VAL SEQRES 5 A 104 SER SER PRO TYR TYR GLU TRP PRO ILE LEU SER SER GLY SEQRES 6 A 104 ASP VAL TYR SER GLY GLY SER PRO GLY ALA ASP ARG VAL SEQRES 7 A 104 VAL PHE ASN GLU ASN ASN GLN LEU ALA GLY VAL ILE THR SEQRES 8 A 104 HIS THR GLY ALA SER GLY ASN ASN PHE VAL GLU CYS THR HET CA A 201 1 HET 2GP A 202 24 HETNAM CA CALCIUM ION HETNAM 2GP GUANOSINE-2'-MONOPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 2GP C10 H14 N5 O8 P FORMUL 4 HOH *79(H2 O) HELIX 1 1 SER A 13 ASP A 29 1 17 SHEET 1 A 2 TYR A 4 CYS A 6 0 SHEET 2 A 2 ASN A 9 TYR A 11 -1 N TYR A 11 O TYR A 4 SHEET 1 B 4 HIS A 40 TYR A 42 0 SHEET 2 B 4 TYR A 56 PRO A 60 -1 N GLU A 58 O HIS A 40 SHEET 3 B 4 ASP A 76 ASN A 81 -1 N PHE A 80 O TYR A 57 SHEET 4 B 4 LEU A 86 THR A 91 -1 N ILE A 90 O ARG A 77 SSBOND 1 CYS A 2 CYS A 10 1555 1555 2.01 SSBOND 2 CYS A 6 CYS A 103 1555 1555 2.04 LINK OD1 ASP A 15 CA CA A 201 1555 1555 2.80 LINK OD2 ASP A 15 CA CA A 201 1555 1555 2.73 LINK CA CA A 201 O HOH A 216 1555 1555 2.85 LINK CA CA A 201 O HOH A 221 1555 1555 2.72 LINK CA CA A 201 O HOH A 225 1555 1555 2.76 LINK CA CA A 201 O HOH A 236 1555 1555 2.92 LINK CA CA A 201 O HOH A 241 1555 1555 2.83 LINK CA CA A 201 O HOH A 291 1555 1555 3.24 CISPEP 1 TYR A 38 PRO A 39 0 -5.01 CISPEP 2 SER A 54 PRO A 55 0 3.58 SITE 1 CAT 5 TYR A 38 HIS A 40 GLU A 58 ARG A 77 SITE 2 CAT 5 HIS A 92 SITE 1 CAL 1 ASP A 15 SITE 1 AC1 6 ASP A 15 HOH A 216 HOH A 221 HOH A 225 SITE 2 AC1 6 HOH A 236 HOH A 241 SITE 1 AC2 12 TYR A 38 HIS A 40 TYR A 42 ASN A 43 SITE 2 AC2 12 ASN A 44 TYR A 45 GLU A 46 GLU A 58 SITE 3 AC2 12 ARG A 77 HIS A 92 ASN A 98 PHE A 100 CRYST1 40.510 48.000 50.810 90.00 90.00 90.00 P 21 21 21 4 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 0.024685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020833 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019681 0.00000