PDB Short entry for 2Z4U HEADER HYDROLASE 26-JUN-07 2Z4U TITLE CRYSTAL STRUCTURE OF WILD TYPE PD-L4 FROM PHYTOLACCA DIOICA LEAVES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN PD-L4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RRNA N- GLYCOSIDASE PD-L3/PD-L4; COMPND 5 EC: 3.2.2.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYTOLACCA DIOICA; SOURCE 3 ORGANISM_TAXID: 29725 KEYWDS RIBOSOME-INACTIVATING PROTEIN, CRYSTALLIZATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RUGGIERO,R.BERISIO REVDAT 3 01-NOV-23 2Z4U 1 REMARK REVDAT 2 24-FEB-09 2Z4U 1 VERSN REVDAT 1 26-FEB-08 2Z4U 0 JRNL AUTH A.RUGGIERO,A.CHAMBERY,A.DI MARO,A.PARENTE,R.BERISIO JRNL TITL ATOMIC RESOLUTION (1.1 A) STRUCTURE OF THE JRNL TITL 2 RIBOSOME-INACTIVATING PROTEIN PD-L4 FROM PHYTOLACCA DIOICA JRNL TITL 3 L. LEAVES JRNL REF PROTEINS V. 71 8 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 17963235 JRNL DOI 10.1002/PROT.21712 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.122 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 103537 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2048 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 591 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027522. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 102812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: IL MILIONE REMARK 200 STARTING MODEL: PDB ENTRY 1QCG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 10% ISOPROPANOL, 0.1M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 21.76050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.38700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.40650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.38700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.76050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.40650 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 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 ASP A 42 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 56 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP A 56 CB - CG - OD2 ANGL. DEV. = -13.6 DEGREES REMARK 500 ARG A 67 CD - NE - CZ ANGL. DEV. = 41.3 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASN A 69 OD1 - CG - ND2 ANGL. DEV. = 15.3 DEGREES REMARK 500 TYR A 72 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR A 86 CB - CG - CD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 LYS A 114 CB - CG - CD ANGL. DEV. = 17.8 DEGREES REMARK 500 ARG A 178 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 192 CD - NE - CZ ANGL. DEV. = 30.2 DEGREES REMARK 500 ARG A 192 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 240 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 THR A 261 C - N - CA ANGL. DEV. = 15.0 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 ASN A 117 46.23 -87.38 REMARK 500 VAL A 173 -72.31 -106.78 REMARK 500 LEU A 228 -165.60 -121.17 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 EDO A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QCG RELATED DB: PDB REMARK 900 RELATED ID: 2Z53 RELATED DB: PDB REMARK 900 RELATED ID: 2QES RELATED DB: PDB REMARK 900 RELATED ID: 2QET RELATED DB: PDB DBREF 2Z4U A 1 261 UNP P84854 RIPL2_PHYDI 1 261 SEQRES 1 A 261 VAL ASN THR ILE THR PHE ASP VAL GLY ASN ALA THR ILE SEQRES 2 A 261 ASN LYS TYR ALA THR PHE MET GLU SER LEU ARG ASN GLU SEQRES 3 A 261 ALA LYS ASP PRO THR LEU LYS CYS TYR GLY ILE PRO MET SEQRES 4 A 261 LEU PRO ASP SER ASN LEU THR PRO LYS TYR VAL LEU VAL SEQRES 5 A 261 LYS LEU GLN ASP ALA SER SER LYS THR ILE THR LEU MET SEQRES 6 A 261 LEU ARG ARG ASN ASN LEU TYR VAL MET GLY TYR SER ASP SEQRES 7 A 261 LEU TYR ASN GLY LYS CYS ARG TYR HIS ILE PHE ASN ASP SEQRES 8 A 261 ILE SER SER THR GLU SER THR ASP VAL GLU ASN THR LEU SEQRES 9 A 261 CYS PRO ASN SER ASN SER ARG GLU LYS LYS ALA ILE ASN SEQRES 10 A 261 TYR ASN SER GLN TYR SER THR LEU GLN ASN LYS ALA GLY SEQRES 11 A 261 VAL SER SER ARG SER GLN VAL GLN LEU GLY ILE GLN ILE SEQRES 12 A 261 LEU ASN SER ASP ILE GLY LYS ILE SER GLY VAL SER THR SEQRES 13 A 261 PHE THR ASP LYS THR GLU ALA GLU PHE LEU LEU VAL ALA SEQRES 14 A 261 ILE GLN MET VAL SER GLU ALA ALA ARG PHE LYS TYR ILE SEQRES 15 A 261 GLU ASN GLN VAL LYS THR ASN PHE ASN ARG ALA PHE ASN SEQRES 16 A 261 PRO ASN PRO LYS VAL LEU SER LEU GLU GLU ASN TRP GLY SEQRES 17 A 261 LYS ILE SER LEU ALA ILE HIS ASN ALA LYS ASN GLY ALA SEQRES 18 A 261 LEU THR SER PRO LEU GLU LEU LYS ASN ALA ASP ASP THR SEQRES 19 A 261 LYS TRP ILE VAL LEU ARG VAL ASP GLU ILE LYS PRO ASP SEQRES 20 A 261 MET GLY LEU LEU ASN TYR VAL SER GLY THR CYS GLN THR SEQRES 21 A 261 THR HET EDO A 501 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *591(H2 O) HELIX 1 1 THR A 12 LYS A 28 1 17 HELIX 2 2 SER A 93 CYS A 105 1 13 HELIX 3 3 GLN A 121 GLY A 130 1 10 HELIX 4 4 SER A 133 VAL A 137 5 5 HELIX 5 5 GLY A 140 SER A 152 1 13 HELIX 6 6 THR A 158 PHE A 179 1 22 HELIX 7 7 PHE A 179 ASN A 189 1 11 HELIX 8 8 ASN A 197 ALA A 217 1 21 HELIX 9 9 VAL A 241 LYS A 245 1 5 HELIX 10 10 PRO A 246 MET A 248 5 3 SHEET 1 A 6 THR A 3 ASP A 7 0 SHEET 2 A 6 TYR A 49 GLN A 55 1 O LYS A 53 N PHE A 6 SHEET 3 A 6 THR A 61 ARG A 67 -1 O LEU A 64 N VAL A 52 SHEET 4 A 6 VAL A 73 TYR A 80 -1 O MET A 74 N MET A 65 SHEET 5 A 6 LYS A 83 ILE A 88 -1 O HIS A 87 N TYR A 76 SHEET 6 A 6 ARG A 111 LYS A 113 1 O GLU A 112 N CYS A 84 SHEET 1 B 2 LYS A 33 CYS A 34 0 SHEET 2 B 2 ILE A 37 PRO A 38 -1 O ILE A 37 N CYS A 34 SHEET 1 C 2 ALA A 221 LYS A 229 0 SHEET 2 C 2 LYS A 235 ARG A 240 -1 O TRP A 236 N LEU A 228 SSBOND 1 CYS A 34 CYS A 258 1555 1555 2.06 SSBOND 2 CYS A 84 CYS A 105 1555 1555 2.06 CISPEP 1 THR A 46 PRO A 47 0 -9.34 CISPEP 2 THR A 260 THR A 261 0 7.00 SITE 1 AC1 8 TYR A 72 SER A 120 TYR A 122 ILE A 170 SITE 2 AC1 8 HOH A1001 HOH A1007 HOH A1062 HOH A1268 CRYST1 43.521 58.813 98.774 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 0.022977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017003 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010124 0.00000