HEADER HYDROLASE 30-AUG-13 3WHO TITLE X-RAY-CRYSTALLOGRAPHIC STRUCTURE OF AN RNASE PO1 EXHIBITING ANTI-TUMOR TITLE 2 ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYL-SPECIFIC RIBONUCLEASE PO1; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: RNASE PO1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS OSTREATUS; SOURCE 3 ORGANISM_COMMON: OYSTER MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5322; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.KOBAYASHI,T.KATSURTANI,Y.HARA,N.MOTOYOSHI,T.ITAGAKI,F.AKITA, AUTHOR 2 A.HIGASHIURA,Y.YAMADA,M.SUZUKI,N.INOKUCHI REVDAT 4 13-NOV-24 3WHO 1 REMARK REVDAT 3 11-OCT-23 3WHO 1 COMPND SOURCE KEYWDS REMARK REVDAT 3 2 1 SEQADV SEQRES HELIX SHEET REVDAT 3 3 1 SSBOND ATOM REVDAT 2 09-OCT-19 3WHO 1 JRNL REVDAT 1 02-JUL-14 3WHO 0 JRNL AUTH H.KOBAYASHI,T.KATSUTANI,Y.HARA,N.MOTOYOSHI,T.ITAGAKI, JRNL AUTH 2 F.AKITA,A.HIGASHIURA,Y.YAMADA,N.INOKUCHI,M.SUZUKI JRNL TITL X-RAY CRYSTALLOGRAPHIC STRUCTURE OF RNASE PO1 THAT EXHIBITS JRNL TITL 2 ANTI-TUMOR ACTIVITY. JRNL REF BIOL.PHARM.BULL. V. 37 968 2014 JRNL REFN ISSN 0918-6158 JRNL PMID 24882409 JRNL DOI 10.1248/BPB.B13-00929 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 18538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 947 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.7300 - 3.5400 1.00 2595 109 0.1917 0.2121 REMARK 3 2 3.5400 - 2.8100 1.00 2554 159 0.2022 0.2671 REMARK 3 3 2.8100 - 2.4500 1.00 2567 140 0.2168 0.2489 REMARK 3 4 2.4500 - 2.2300 1.00 2587 124 0.2029 0.2426 REMARK 3 5 2.2300 - 2.0700 1.00 2560 158 0.2015 0.2614 REMARK 3 6 2.0700 - 1.9500 1.00 2543 140 0.1999 0.2674 REMARK 3 7 1.9500 - 1.8500 0.84 2185 117 0.2240 0.2824 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.220 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2335 REMARK 3 ANGLE : 0.962 3166 REMARK 3 CHIRALITY : 0.056 320 REMARK 3 PLANARITY : 0.011 434 REMARK 3 DIHEDRAL : 10.741 791 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000096347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 37.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.15700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: 2BU4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, 0.1M BIS-TRIS REMARK 280 PROPANE, 10% PEG400, 0.75M CESIUM CHLORIDE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 11.60100 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 23.20200 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 OD1 ASN A 94 O HOH A 244 1.96 REMARK 500 O HOH B 201 O HOH B 220 1.99 REMARK 500 O HOH C 201 O HOH C 223 2.03 REMARK 500 O HOH A 201 O HOH A 222 2.05 REMARK 500 OG SER A 13 O HOH A 229 2.10 REMARK 500 OE2 GLU C 42 O HOH C 215 2.14 REMARK 500 OE1 GLN C 1 NH2 ARG C 27 2.17 REMARK 500 O HOH B 212 O HOH B 227 2.17 REMARK 500 NH2 ARG A 80 O THR B 88 2.19 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 SER A 47 40.08 -82.64 REMARK 500 PRO B 91 24.62 -79.59 REMARK 500 SER C 47 38.77 -82.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 3WHO A 1 101 UNP P81762 RNPO_PLEOS 1 101 DBREF 3WHO B 1 101 UNP P81762 RNPO_PLEOS 1 101 DBREF 3WHO C 1 101 UNP P81762 RNPO_PLEOS 1 101 SEQADV 3WHO SER A 100 UNP P81762 ARG 100 VARIANT SEQADV 3WHO SER B 100 UNP P81762 ARG 100 VARIANT SEQADV 3WHO SER C 100 UNP P81762 ARG 100 VARIANT SEQRES 1 A 101 GLN THR GLY VAL ARG SER CYS ASN CYS ALA GLY ARG SER SEQRES 2 A 101 PHE THR GLY THR ASP VAL THR ASN ALA ILE ARG SER ALA SEQRES 3 A 101 ARG ALA GLY GLY SER GLY ASN TYR PRO HIS VAL TYR ASN SEQRES 4 A 101 ASN PHE GLU GLY PHE SER PHE SER CYS THR PRO THR PHE SEQRES 5 A 101 PHE GLU PHE PRO VAL PHE ARG GLY SER VAL TYR SER GLY SEQRES 6 A 101 GLY SER PRO GLY ALA ASP ARG VAL ILE TYR ASP GLN SER SEQRES 7 A 101 GLY ARG PHE CYS ALA CYS LEU THR HIS THR GLY ALA PRO SEQRES 8 A 101 SER THR ASN GLY PHE VAL GLU CYS SER PHE SEQRES 1 B 101 GLN THR GLY VAL ARG SER CYS ASN CYS ALA GLY ARG SER SEQRES 2 B 101 PHE THR GLY THR ASP VAL THR ASN ALA ILE ARG SER ALA SEQRES 3 B 101 ARG ALA GLY GLY SER GLY ASN TYR PRO HIS VAL TYR ASN SEQRES 4 B 101 ASN PHE GLU GLY PHE SER PHE SER CYS THR PRO THR PHE SEQRES 5 B 101 PHE GLU PHE PRO VAL PHE ARG GLY SER VAL TYR SER GLY SEQRES 6 B 101 GLY SER PRO GLY ALA ASP ARG VAL ILE TYR ASP GLN SER SEQRES 7 B 101 GLY ARG PHE CYS ALA CYS LEU THR HIS THR GLY ALA PRO SEQRES 8 B 101 SER THR ASN GLY PHE VAL GLU CYS SER PHE SEQRES 1 C 101 GLN THR GLY VAL ARG SER CYS ASN CYS ALA GLY ARG SER SEQRES 2 C 101 PHE THR GLY THR ASP VAL THR ASN ALA ILE ARG SER ALA SEQRES 3 C 101 ARG ALA GLY GLY SER GLY ASN TYR PRO HIS VAL TYR ASN SEQRES 4 C 101 ASN PHE GLU GLY PHE SER PHE SER CYS THR PRO THR PHE SEQRES 5 C 101 PHE GLU PHE PRO VAL PHE ARG GLY SER VAL TYR SER GLY SEQRES 6 C 101 GLY SER PRO GLY ALA ASP ARG VAL ILE TYR ASP GLN SER SEQRES 7 C 101 GLY ARG PHE CYS ALA CYS LEU THR HIS THR GLY ALA PRO SEQRES 8 C 101 SER THR ASN GLY PHE VAL GLU CYS SER PHE FORMUL 4 HOH *137(H2 O) HELIX 1 AA1 THR A 15 ALA A 28 1 14 HELIX 2 AA2 THR B 15 ALA B 28 1 14 HELIX 3 AA3 THR C 15 ALA C 28 1 14 SHEET 1 AA1 2 CYS A 7 CYS A 9 0 SHEET 2 AA1 2 ARG A 12 PHE A 14 -1 O PHE A 14 N CYS A 7 SHEET 1 AA2 5 HIS A 36 TYR A 38 0 SHEET 2 AA2 5 PHE A 52 PRO A 56 -1 O PHE A 52 N TYR A 38 SHEET 3 AA2 5 ASP A 71 ASP A 76 -1 O TYR A 75 N PHE A 53 SHEET 4 AA2 5 PHE A 81 THR A 86 -1 O CYS A 82 N ILE A 74 SHEET 5 AA2 5 VAL A 97 GLU A 98 -1 O VAL A 97 N THR A 86 SHEET 1 AA3 2 CYS B 7 CYS B 9 0 SHEET 2 AA3 2 ARG B 12 PHE B 14 -1 O PHE B 14 N CYS B 7 SHEET 1 AA4 5 HIS B 36 TYR B 38 0 SHEET 2 AA4 5 PHE B 52 PRO B 56 -1 O PHE B 52 N TYR B 38 SHEET 3 AA4 5 ASP B 71 ASP B 76 -1 O TYR B 75 N PHE B 53 SHEET 4 AA4 5 PHE B 81 THR B 86 -1 O CYS B 82 N ILE B 74 SHEET 5 AA4 5 VAL B 97 GLU B 98 -1 O VAL B 97 N THR B 86 SHEET 1 AA5 2 CYS C 7 CYS C 9 0 SHEET 2 AA5 2 ARG C 12 PHE C 14 -1 O PHE C 14 N CYS C 7 SHEET 1 AA6 5 HIS C 36 TYR C 38 0 SHEET 2 AA6 5 PHE C 52 PRO C 56 -1 O GLU C 54 N HIS C 36 SHEET 3 AA6 5 ASP C 71 ASP C 76 -1 O TYR C 75 N PHE C 53 SHEET 4 AA6 5 PHE C 81 THR C 86 -1 O CYS C 82 N ILE C 74 SHEET 5 AA6 5 VAL C 97 GLU C 98 -1 O VAL C 97 N THR C 86 SSBOND 1 CYS A 7 CYS A 84 1555 1555 2.02 SSBOND 2 CYS A 9 CYS A 99 1555 1555 2.04 SSBOND 3 CYS A 48 CYS A 82 1555 1555 2.04 SSBOND 4 CYS B 7 CYS B 84 1555 1555 2.02 SSBOND 5 CYS B 9 CYS B 99 1555 1555 2.06 SSBOND 6 CYS B 48 CYS B 82 1555 1555 2.05 SSBOND 7 CYS C 7 CYS C 84 1555 1555 2.04 SSBOND 8 CYS C 9 CYS C 99 1555 1555 2.06 SSBOND 9 CYS C 48 CYS C 82 1555 1555 2.02 CISPEP 1 TYR A 34 PRO A 35 0 -0.10 CISPEP 2 PRO A 50 THR A 51 0 7.68 CISPEP 3 TYR B 34 PRO B 35 0 -0.80 CISPEP 4 PRO B 50 THR B 51 0 5.75 CISPEP 5 TYR C 34 PRO C 35 0 0.27 CISPEP 6 PRO C 50 THR C 51 0 6.61 CRYST1 75.557 75.557 34.803 90.00 90.00 120.00 P 31 9 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 0.013235 0.007641 0.000000 0.00000 SCALE2 0.000000 0.015283 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028733 0.00000