HEADER ALLERGEN 22-AUG-03 1Q9B TITLE CRYSTAL STRUCTURE ANALYSIS OF HEV B 6.02 (HEVEIN) AT 1.5 ANGSTROMS TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEVEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEV B 6.02 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS; SOURCE 3 ORGANISM_TAXID: 3981; SOURCE 4 TISSUE: LATEX KEYWDS ALLERGEN, LECTIN, AGGLUTININ-TOXIN MOTIF EXPDTA X-RAY DIFFRACTION AUTHOR A.RODRIGUEZ-ROMERO,A.HERNANDEZ-SANTOYO REVDAT 4 24-JUL-19 1Q9B 1 REMARK REVDAT 3 11-OCT-17 1Q9B 1 REMARK REVDAT 2 24-FEB-09 1Q9B 1 VERSN REVDAT 1 13-JAN-04 1Q9B 0 JRNL AUTH C.A.REYES-LOPEZ,A.HERNANDEZ-SANTOYO,M.PEDRAZA-ESCALONA, JRNL AUTH 2 G.MENDOZA,A.HERNANDEZ-ARANA,A.RODRIGUEZ-ROMERO JRNL TITL INSIGHTS INTO A CONFORMATIONAL EPITOPE OF HEV B 6.02 JRNL TITL 2 (HEVEIN). JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 314 123 2004 JRNL REFN ISSN 0006-291X JRNL PMID 14715255 JRNL DOI 10.1016/J.BBRC.2003.12.068 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.RODRIGUEZ-ROMERO,K.G.RAVICHANDRAN,M.SORIANO-GARCIA REMARK 1 TITL CRYSTAL STRUCTURE OF HEVEIN AT 2.8 A RESOLUTION REMARK 1 REF FEBS LETT. V. 291 307 1991 REMARK 1 REFN ISSN 0014-5793 REMARK 1 DOI 10.1016/0014-5793(91)81308-U REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.128 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 698 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6996 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.128 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.128 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 680 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6809 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 379.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 268.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 8 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3772 REMARK 3 NUMBER OF RESTRAINTS : 4884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.021 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.060 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.077 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.021 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.034 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.065 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ALTERNATE CONFORMATIONS EVENTUALLY REMARK 3 REDUCED FREE R FROM 21.19-19.20%. INTRODUCTION OF ANISOTROPIC REMARK 3 REFINEMENT REDUCED FREE R FROM 19.20- 16.01%. DISCRETELY REMARK 3 DISORDERED HETEROGENS: 2, MPD 101 AND MPD 102; DISCRETELY REMARK 3 DISORDERED RESIDUES: 6, GLU 1, LEU 11, PRO 13, SER 26, GLU 29, REMARK 3 PRO 33. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, REMARK 3 MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1Q9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-03. REMARK 100 THE DEPOSITION ID IS D_1000020078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-99 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 7.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AGROVATA, TRUNCATE, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.04600 REMARK 200 FOR SHELL : 12.30 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: PDB ENTRY 1HEV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, TRIS-HCL, PH 7.10, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 15.90500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.47500 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 28 CB - CG - OD2 ANGL. DEV. = -7.0 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 ALA A 7 47.32 -144.86 REMARK 500 LYS A 42 -164.32 -103.91 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 MPD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 102 DBREF 1Q9B A 1 43 UNP P02877 HEVE_HEVBR 18 60 SEQRES 1 A 43 GLU GLN CYS GLY ARG GLN ALA GLY GLY LYS LEU CYS PRO SEQRES 2 A 43 ASN ASN LEU CYS CYS SER GLN TRP GLY TRP CYS GLY SER SEQRES 3 A 43 THR ASP GLU TYR CYS SER PRO ASP HIS ASN CYS GLN SER SEQRES 4 A 43 ASN CYS LYS ASP HET MPD A 101 16 HET MPD A 102 16 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 2(C6 H14 O2) FORMUL 4 HOH *39(H2 O) HELIX 1 1 CYS A 3 GLY A 8 5 6 HELIX 2 2 CYS A 12 LEU A 16 5 5 HELIX 3 3 THR A 27 SER A 32 1 6 HELIX 4 4 PRO A 33 ASN A 36 5 4 SHEET 1 A 2 CYS A 17 CYS A 18 0 SHEET 2 A 2 CYS A 24 GLY A 25 -1 O GLY A 25 N CYS A 17 SSBOND 1 CYS A 3 CYS A 18 1555 1555 2.04 SSBOND 2 CYS A 12 CYS A 24 1555 1555 2.03 SSBOND 3 CYS A 17 CYS A 31 1555 1555 2.02 SSBOND 4 CYS A 37 CYS A 41 1555 1555 2.02 SITE 1 AC1 8 LEU A 11 PRO A 13 TRP A 21 SER A 39 SITE 2 AC1 8 ASN A 40 HOH A 207 HOH A 220 HOH A 224 SITE 1 AC2 7 ARG A 5 ASN A 15 TRP A 23 GLU A 29 SITE 2 AC2 7 TYR A 30 ASN A 40 HOH A 204 CRYST1 31.810 60.950 22.510 90.00 90.00 90.00 P 21 21 2 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 0.031437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044425 0.00000