HEADER HYDROLASE 23-MAY-12 4FBH TITLE STRUCTURE OF RIP FROM BARLEY SEEDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SYNTHESIS INHIBITOR I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBOSOME-INACTIVATING PROTEIN I, RRNA N-GLYCOSIDASE; COMPND 5 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; SOURCE 3 ORGANISM_COMMON: BARLEY; SOURCE 4 ORGANISM_TAXID: 4513; SOURCE 5 TISSUE: SEED KEYWDS HYDROLASE, RIBOSOME INACTIVATING PROTEIN, RRNA N-GLYCOSYLASE KEYWDS 2 ACTIVITY, RIBOSOME EXPDTA X-RAY DIFFRACTION AUTHOR B.-G.LEE,M.K.KIM,S.W.SUH,H.K.SONG REVDAT 4 13-SEP-23 4FBH 1 REMARK REVDAT 3 15-NOV-17 4FBH 1 REMARK REVDAT 2 23-JAN-13 4FBH 1 JRNL REVDAT 1 31-OCT-12 4FBH 0 JRNL AUTH B.G.LEE,M.K.KIM,B.W.KIM,S.W.SUH,H.K.SONG JRNL TITL STRUCTURES OF THE RIBOSOME-INACTIVATING PROTEIN FROM BARLEY JRNL TITL 2 SEEDS REVEAL A UNIQUE ACTIVATION MECHANISM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 1488 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 23090398 JRNL DOI 10.1107/S0907444912037110 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 11804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1213 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 25.4829 - 4.7751 0.89 1119 138 0.1914 0.2263 REMARK 3 2 4.7751 - 3.7942 0.91 1107 143 0.1511 0.2017 REMARK 3 3 3.7942 - 3.3157 0.97 1179 147 0.1629 0.2384 REMARK 3 4 3.3157 - 3.0131 0.99 1235 127 0.1797 0.2302 REMARK 3 5 3.0131 - 2.7974 1.00 1241 130 0.1855 0.2731 REMARK 3 6 2.7974 - 2.6327 0.99 1233 121 0.1885 0.2799 REMARK 3 7 2.6327 - 2.5009 0.98 1150 166 0.2017 0.2975 REMARK 3 8 2.5009 - 2.3922 0.95 1179 124 0.1987 0.2953 REMARK 3 9 2.3922 - 2.3000 0.93 1148 117 0.1926 0.2943 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 : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.730 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) : 0.88550 REMARK 3 B22 (A**2) : 9.60230 REMARK 3 B33 (A**2) : -9.64120 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.82880 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 2088 REMARK 3 ANGLE : 1.107 2844 REMARK 3 CHIRALITY : 0.062 327 REMARK 3 PLANARITY : 0.006 364 REMARK 3 DIHEDRAL : 12.654 752 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 4FBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-92 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 8.41 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROFILE FITTING PROCEDURE REMARK 200 DATA SCALING SOFTWARE : FOURIER REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 32.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.4 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4FB9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 27.5 %(W/V) PEG 1500, REMARK 280 PH 8.41, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 44.18000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.18000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.29500 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 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 193 REMARK 465 ALA A 194 REMARK 465 VAL A 195 REMARK 465 GLU A 196 REMARK 465 LYS A 197 REMARK 465 PRO A 229 REMARK 465 GLY A 230 REMARK 465 LYS A 231 REMARK 465 SER A 232 REMARK 465 PRO A 233 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 LYS A 4 CG CD CE NZ REMARK 470 LYS A 198 CG CD CE NZ 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 PRO A 56 C - N - CA ANGL. DEV. = 11.1 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 PRO A 56 -76.97 -32.77 REMARK 500 VAL A 173 -67.62 -108.39 REMARK 500 REMARK 500 REMARK: NULL 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FB9 RELATED DB: PDB REMARK 900 RELATED ID: 4FBA RELATED DB: PDB REMARK 900 RELATED ID: 4FBB RELATED DB: PDB REMARK 900 RELATED ID: 4FBC RELATED DB: PDB DBREF 4FBH A 1 281 UNP P22244 RIP1_HORVU 1 281 SEQRES 1 A 281 MET ALA ALA LYS MET ALA LYS ASN VAL ASP LYS PRO LEU SEQRES 2 A 281 PHE THR ALA THR PHE ASN VAL GLN ALA SER SER ALA ASP SEQRES 3 A 281 TYR ALA THR PHE ILE ALA GLY ILE ARG ASN LYS LEU ARG SEQRES 4 A 281 ASN PRO ALA HIS PHE SER HIS ASN ARG PRO VAL LEU PRO SEQRES 5 A 281 PRO VAL GLU PRO ASN VAL PRO PRO SER ARG TRP PHE HIS SEQRES 6 A 281 VAL VAL LEU LYS ALA SER PRO THR SER ALA GLY LEU THR SEQRES 7 A 281 LEU ALA ILE ARG ALA ASP ASN ILE TYR LEU GLU GLY PHE SEQRES 8 A 281 LYS SER SER ASP GLY THR TRP TRP GLU LEU THR PRO GLY SEQRES 9 A 281 LEU ILE PRO GLY ALA THR TYR VAL GLY PHE GLY GLY THR SEQRES 10 A 281 TYR ARG ASP LEU LEU GLY ASP THR ASP LYS LEU THR ASN SEQRES 11 A 281 VAL ALA LEU GLY ARG GLN GLN LEU ALA ASP ALA VAL THR SEQRES 12 A 281 ALA LEU HIS GLY ARG THR LYS ALA ASP LYS PRO SER GLY SEQRES 13 A 281 PRO LYS GLN GLN GLN ALA ARG GLU ALA VAL THR THR LEU SEQRES 14 A 281 LEU LEU MET VAL ASN GLU ALA THR ARG PHE GLN THR VAL SEQRES 15 A 281 SER GLY PHE VAL ALA GLY LEU LEU HIS PRO LYS ALA VAL SEQRES 16 A 281 GLU LYS LYS SER GLY LYS ILE GLY ASN GLU MET LYS ALA SEQRES 17 A 281 GLN VAL ASN GLY TRP GLN ASP LEU SER ALA ALA LEU LEU SEQRES 18 A 281 LYS THR ASP VAL LYS PRO PRO PRO GLY LYS SER PRO ALA SEQRES 19 A 281 LYS PHE ALA PRO ILE GLU LYS MET GLY VAL ARG THR ALA SEQRES 20 A 281 VAL GLN ALA ALA ASN THR LEU GLY ILE LEU LEU PHE VAL SEQRES 21 A 281 GLU VAL PRO GLY GLY LEU THR VAL ALA LYS ALA LEU GLU SEQRES 22 A 281 LEU PHE HIS ALA SER GLY GLY LYS HET AMP A 301 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *92(H2 O) HELIX 1 1 SER A 23 ARG A 39 1 17 HELIX 2 2 THR A 117 GLY A 123 1 7 HELIX 3 3 ASP A 124 VAL A 131 5 8 HELIX 4 4 ARG A 135 GLY A 147 1 13 HELIX 5 5 THR A 149 LYS A 153 5 5 HELIX 6 6 SER A 155 VAL A 173 1 19 HELIX 7 7 VAL A 173 PHE A 179 1 7 HELIX 8 8 PHE A 179 LEU A 190 1 12 HELIX 9 9 GLY A 203 ASN A 211 1 9 HELIX 10 10 GLY A 212 THR A 223 1 12 HELIX 11 11 ILE A 239 GLY A 243 5 5 HELIX 12 12 THR A 246 LEU A 254 1 9 HELIX 13 13 THR A 267 SER A 278 1 12 SHEET 1 A 6 THR A 15 ASN A 19 0 SHEET 2 A 6 TRP A 63 LYS A 69 1 O HIS A 65 N ALA A 16 SHEET 3 A 6 LEU A 77 ARG A 82 -1 O LEU A 79 N VAL A 66 SHEET 4 A 6 LEU A 88 LYS A 92 -1 O GLY A 90 N ALA A 80 SHEET 5 A 6 TRP A 98 GLU A 100 -1 O TRP A 99 N PHE A 91 SHEET 6 A 6 THR A 110 TYR A 111 1 O THR A 110 N TRP A 98 SHEET 1 B 2 PHE A 44 SER A 45 0 SHEET 2 B 2 ARG A 48 PRO A 49 -1 O ARG A 48 N SER A 45 SHEET 1 C 2 LEU A 133 GLY A 134 0 SHEET 2 C 2 SER A 199 GLY A 200 -1 O GLY A 200 N LEU A 133 SITE 1 AC1 8 TYR A 87 LEU A 88 LYS A 150 ARG A 178 SITE 2 AC1 8 HOH A 421 HOH A 438 HOH A 456 HOH A 466 CRYST1 88.360 62.590 53.180 90.00 108.62 90.00 C 1 2 1 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 0.011317 0.000000 0.003813 0.00000 SCALE2 0.000000 0.015977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019843 0.00000