PDB Short entry for 1WUW HEADER PLANT PROTEIN 09-DEC-04 1WUW TITLE CRYSTAL STRUCTURE OF BETA HORDOTHIONIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-HORDOTHIONIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HORDEUM VULGARE; SOURCE 3 ORGANISM_TAXID: 4513 KEYWDS CRAMBIN FOLD, DIMER, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.A.JOHNSON,E.KIM,M.M.TEETER,S.W.SUH,B.STEC REVDAT 7 25-OCT-23 1WUW 1 REMARK REVDAT 6 04-AUG-21 1WUW 1 REMARK REVDAT 5 11-OCT-17 1WUW 1 REMARK REVDAT 4 01-SEP-10 1WUW 1 JRNL REVDAT 3 24-FEB-09 1WUW 1 VERSN REVDAT 2 06-DEC-05 1WUW 1 TITLE JRNL REVDAT 1 11-JAN-05 1WUW 0 JRNL AUTH K.A.JOHNSON,E.KIM,M.M.TEETER,S.W.SUH,B.STEC JRNL TITL CRYSTAL STRUCTURE OF ALPHA-HORDOTHIONIN AT 1.9 ANGSTROM JRNL TITL 2 RESOLUTION. JRNL REF FEBS LETT. V. 579 2301 2005 JRNL REFN ISSN 0014-5793 JRNL PMID 15848162 JRNL DOI 10.1016/J.FEBSLET.2004.12.100 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.172 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 465 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8963 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 : 674 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 92 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) : 0.032 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 1WUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000024028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-94 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.6 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) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8963 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 15.10 REMARK 200 R MERGE (I) : 0.07800 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1BHP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000, CITRATE, AMMONIUM SULFATE, REMARK 280 TOLUENE SULFATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 23.73500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.33000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.86750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.33000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.60250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.33000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.86750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.33000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.60250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.73500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 256 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 275 LIES ON A SPECIAL POSITION. 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 ARG A 30 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 30 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 60 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN B 61 0.09 SIDE CHAIN 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 TSU A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TSU B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SER B 105 DBREF 1WUW A 1 45 UNP P21742 THNB_HORVU 28 72 DBREF 1WUW B 51 95 UNP P21742 THNB_HORVU 28 72 SEQRES 1 A 45 LYS SER CYS CYS ARG SER THR LEU GLY ARG ASN CYS TYR SEQRES 2 A 45 ASN LEU CYS ARG VAL ARG GLY ALA GLN LYS LEU CYS ALA SEQRES 3 A 45 ASN ALA CYS ARG CYS LYS LEU THR SER GLY LEU LYS CYS SEQRES 4 A 45 PRO SER SER PHE PRO LYS SEQRES 1 B 45 LYS SER CYS CYS ARG SER THR LEU GLY ARG ASN CYS TYR SEQRES 2 B 45 ASN LEU CYS ARG VAL ARG GLY ALA GLN LYS LEU CYS ALA SEQRES 3 B 45 ASN ALA CYS ARG CYS LYS LEU THR SER GLY LEU LYS CYS SEQRES 4 B 45 PRO SER SER PHE PRO LYS HET TSU A 101 11 HET SER A 103 7 HET TSU B 102 11 HET SER B 105 7 HETNAM TSU PARA-TOLUENE SULFONATE HETNAM SER SERINE FORMUL 3 TSU 2(C7 H8 O3 S) FORMUL 4 SER 2(C3 H7 N O3) FORMUL 7 HOH *92(H2 O) HELIX 1 1 SER A 6 ARG A 17 1 12 HELIX 2 2 ALA A 21 ARG A 30 1 10 HELIX 3 3 SER B 56 ARG B 67 1 12 HELIX 4 4 ALA B 71 ARG B 80 1 10 SHEET 1 A 2 SER A 2 CYS A 3 0 SHEET 2 A 2 LYS A 32 LEU A 33 -1 O LYS A 32 N CYS A 3 SHEET 1 B 2 SER B 52 CYS B 53 0 SHEET 2 B 2 LYS B 82 LEU B 83 -1 O LYS B 82 N CYS B 53 SSBOND 1 CYS A 3 CYS A 39 1555 1555 2.04 SSBOND 2 CYS A 4 CYS A 31 1555 1555 2.04 SSBOND 3 CYS A 12 CYS A 29 1555 1555 2.01 SSBOND 4 CYS A 16 CYS A 25 1555 1555 2.03 SSBOND 5 CYS B 53 CYS B 89 1555 1555 2.03 SSBOND 6 CYS B 54 CYS B 81 1555 1555 2.06 SSBOND 7 CYS B 62 CYS B 79 1555 1555 2.02 SSBOND 8 CYS B 66 CYS B 75 1555 1555 2.02 SITE 1 AC1 10 ARG A 5 SER A 6 LEU A 8 GLY A 9 SITE 2 AC1 10 ARG A 30 HOH A 203 ARG B 69 ALA B 78 SITE 3 AC1 10 ARG B 80 TSU B 102 SITE 1 AC2 12 ALA A 28 ARG A 30 TSU A 101 ARG B 55 SITE 2 AC2 12 SER B 56 LEU B 58 GLY B 59 VAL B 68 SITE 3 AC2 12 CYS B 79 ARG B 80 HOH B 216 HOH B 224 SITE 1 AC3 4 SER A 2 TYR A 13 ARG A 17 GLN A 22 SITE 1 AC4 4 LYS B 51 SER B 52 TYR B 63 ARG B 67 CRYST1 68.660 68.660 47.470 90.00 90.00 90.00 P 41 21 2 16 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 0.014565 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021066 0.00000