PDB Short entry for 1NIO HEADER HYDROLASE 24-DEC-02 1NIO TITLE CRYSTAL STRUCTURE OF BETA-LUFFIN, A RIBOSOME INACTIVATING PROTEIN AT TITLE 2 2.0A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: B-LUFFIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-247; COMPND 5 SYNONYM: BETA-LUFFIN; COMPND 6 EC: 3.2.2.22; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUFFA AEGYPTIACA; SOURCE 3 ORGANISM_COMMON: SMOOTH LOOFAH; SOURCE 4 ORGANISM_TAXID: 3670; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSOME INACTIVATING PROTEIN(RIP), BETA-LUFFIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.WU REVDAT 4 29-JUL-20 1NIO 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 1NIO 1 VERSN REVDAT 2 24-FEB-09 1NIO 1 VERSN REVDAT 1 05-AUG-03 1NIO 0 JRNL AUTH Q.J.MA,J.H.LI,H.G.LI,S.WU,Y.C.DONG JRNL TITL CRYSTAL STRUCTURE OF BETA-LUFFIN, A RIBOSOME-INACTIVATING JRNL TITL 2 PROTEIN, AT 2.0 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1366 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12876337 JRNL DOI 10.1107/S0907444903011156 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 341791.350 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 16425 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 SET) : 0.162 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1639 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1352 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 157 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1911 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.140 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.540 ; 3.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 49.54 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000017901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 290 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL 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 : 60278 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11100 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11100 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 44.95100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.91150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.95100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.91150 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 350 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 351 LIES ON A SPECIAL POSITION. 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 ILE A 246 O ILE A 246 2557 2.05 REMARK 500 CB ALA A 247 CB ALA A 247 2557 2.14 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 ASN A 78 -119.63 52.95 REMARK 500 THR A 158 -71.21 -113.58 REMARK 500 ASN A 236 -71.82 -161.46 REMARK 500 ILE A 246 -87.20 -106.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NIO A 1 247 UNP P22851 RIPB_LUFCY 22 268 SEQADV 1NIO LYS A 173 UNP P22851 GLU 194 CONFLICT SEQRES 1 A 247 ALA ASN VAL SER PHE SER LEU SER GLY ALA ASP SER LYS SEQRES 2 A 247 SER TYR SER LYS PHE ILE THR ALA LEU ARG LYS ALA LEU SEQRES 3 A 247 PRO SER LYS GLU LYS VAL SER ASN ILE PRO LEU LEU LEU SEQRES 4 A 247 PRO SER ALA SER GLY ALA SER ARG TYR ILE LEU MET GLN SEQRES 5 A 247 LEU SER ASN TYR ASP ALA LYS ALA ILE THR MET ALA ILE SEQRES 6 A 247 ASP VAL THR ASN VAL TYR ILE MET GLY TYR LEU VAL ASN SEQRES 7 A 247 SER THR SER TYR PHE PHE ASN GLU SER ASP ALA LYS LEU SEQRES 8 A 247 ALA SER GLN TYR VAL PHE LYS GLY SER THR ILE VAL THR SEQRES 9 A 247 LEU PRO TYR SER GLY ASN TYR GLU ARG LEU GLN ASN ALA SEQRES 10 A 247 ALA GLY LYS VAL ARG GLU LYS ILE PRO LEU GLY PHE ARG SEQRES 11 A 247 ALA PHE ASP SER ALA ILE THR SER LEU PHE HIS TYR ASP SEQRES 12 A 247 SER THR ALA ALA ALA GLY ALA PHE LEU VAL ILE ILE GLN SEQRES 13 A 247 THR THR ALA GLU ALA SER ARG PHE LYS TYR ILE GLU GLY SEQRES 14 A 247 GLN ILE ILE LYS ARG ILE PRO LYS ASN GLU VAL PRO SER SEQRES 15 A 247 PRO ALA ALA LEU SER LEU GLU ASN GLU TRP SER ALA LEU SEQRES 16 A 247 SER LYS GLN ILE GLN LEU ALA GLN THR ASN ASN GLY ALA SEQRES 17 A 247 PHE ARG THR PRO VAL VAL ILE ILE ASP ASN LYS GLY GLN SEQRES 18 A 247 ARG VAL GLU ILE LYS ASP VAL ASN SER LYS VAL VAL THR SEQRES 19 A 247 ASN ASN ILE LYS LEU LEU LEU ASN LYS GLN ASN ILE ALA MODRES 1NIO ASN A 2 ASN GLYCOSYLATION SITE MODRES 1NIO ASN A 78 ASN GLYCOSYLATION SITE MODRES 1NIO ASN A 85 ASN GLYCOSYLATION SITE HET NAG A 248 14 HET NAG A 249 14 HET NAG A 250 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 5 HOH *128(H2 O) HELIX 1 1 ASP A 11 LEU A 26 1 16 HELIX 2 2 SER A 43 SER A 46 5 4 HELIX 3 3 GLU A 86 SER A 93 1 8 HELIX 4 4 ASN A 110 GLY A 119 1 10 HELIX 5 5 VAL A 121 ILE A 125 5 5 HELIX 6 6 GLY A 128 HIS A 141 1 14 HELIX 7 7 ALA A 146 THR A 158 1 13 HELIX 8 8 THR A 158 PHE A 164 1 7 HELIX 9 9 PHE A 164 ARG A 174 1 11 HELIX 10 10 SER A 182 GLN A 203 1 22 HELIX 11 11 SER A 230 ASN A 235 1 6 HELIX 12 12 ASN A 242 ILE A 246 5 5 SHEET 1 A 6 VAL A 3 SER A 6 0 SHEET 2 A 6 TYR A 48 SER A 54 1 O GLN A 52 N VAL A 3 SHEET 3 A 6 ALA A 60 ASP A 66 -1 O MET A 63 N MET A 51 SHEET 4 A 6 ILE A 72 VAL A 77 -1 O LEU A 76 N THR A 62 SHEET 5 A 6 THR A 80 PHE A 83 -1 O TYR A 82 N TYR A 75 SHEET 6 A 6 THR A 101 THR A 104 1 O VAL A 103 N SER A 81 SHEET 1 B 2 SER A 28 VAL A 32 0 SHEET 2 B 2 ILE A 35 LEU A 38 -1 O LEU A 37 N GLU A 30 SHEET 1 C 2 ALA A 208 ILE A 216 0 SHEET 2 C 2 ARG A 222 ASP A 227 -1 O ILE A 225 N VAL A 213 LINK ND2 ASN A 2 C1 NAG A 248 1555 1555 1.45 LINK ND2 ASN A 78 C1 NAG A 249 1555 1555 1.45 LINK ND2 ASN A 85 C1 NAG A 250 1555 1555 1.45 CRYST1 89.902 59.823 55.184 90.00 120.81 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 0.011123 0.000000 0.006634 0.00000 SCALE2 0.000000 0.016716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021099 0.00000