HEADER PLANT PROTEIN 10-SEP-01 1JXY TITLE CRAMBIN MIXED SEQUENCE FORM AT 220 K. PROTEIN/WATER SUBSTATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRAMBIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA; SOURCE 3 ORGANISM_TAXID: 3721; SOURCE 4 STRAIN: SUBSP. ABYSSINICA KEYWDS WATER, SUBSTATE, FUNCTION, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.M.TEETER,A.YAMANO,B.STEC,U.MOHANTY REVDAT 3 13-JUL-11 1JXY 1 VERSN REVDAT 2 24-FEB-09 1JXY 1 VERSN REVDAT 1 31-OCT-01 1JXY 0 JRNL AUTH M.M.TEETER,A.YAMANO,B.STEC,U.MOHANTY JRNL TITL ON THE NATURE OF A GLASSY STATE OF MATTER IN A HYDRATED JRNL TITL 2 PROTEIN: RELATION TO PROTEIN FUNCTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 11242 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11572978 JRNL DOI 10.1073/PNAS.201404398 REMARK 2 REMARK 2 RESOLUTION. 0.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 22753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : DIFFERENCE DENSITY PEAKS REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 4.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.06 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 17.67 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.032 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.054 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : 0.005 ; 0.010 REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.009 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.055 ; 0.050 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.148 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : 0.129 ; 0.500 REMARK 3 H-BOND (X-H...Y) (A) : 0.072 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 5.000 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 9.500 ; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 14.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.118 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.121 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.145 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.148 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: OVERALL WEIGHT WAS 1/(SIGDEL) AND REMARK 3 SIGDEL=8-10(SINTH/L-0.166667). WITH PROLSQ, NO RFREE WAS REMARK 3 CALCULATED. ********* STEREOCHEMISTRY REMARKS: BECAUSE DISCRETELY REMARK 3 DISORDERED (MULTIPLE SUBSTATE) PROTEIN RESIDUES EACH HAVE REMARK 3 OCCUPANCY LESS THAN ONE, THEY ARE DIFFICULT TO ACCURATELY REFINE. REMARK 3 THE GEOMETRY CAN BE DISTORTED (IS POORLY DETERMINED). IN THE CASE REMARK 3 OF THR39, THE BACKBONE IS CLEARLY DISORDERED, WITH VERY SMALL REMARK 3 DEVIATIONS BETWEEN SUBSTATES (~0.1 A), AND THAT WAS NOT INCLUDED REMARK 3 IN THE MODEL. HENCE THERE MAY BE LARGE ERRORS INVOLVING CA. REMARK 4 REMARK 4 1JXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-01. REMARK 100 THE RCSB ID CODE IS RCSB014314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-90 REMARK 200 TEMPERATURE (KELVIN) : 220.0 REMARK 200 PH : 7.00 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 : MO REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : RIGAKU AFC-5R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : LEHMANN-LARSEN REMARK 200 DATA SCALING SOFTWARE : TEXSAN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27080 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 17.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.7 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1JXX, CRAMBIN MIXED FORM AT 200 K. REMARK 200 REMARK 200 REMARK: VALUES OF F/SIGF ARE GIVEN ABOVE RATHER THAN I/SIGI. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHANOL, PH 7.00, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 9.28000 REMARK 290 SMTRY3 2 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 300 REMARK: NOT KNOWN BUT MAY BE MONOMER 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: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 8 24.0 L L OUTSIDE RANGE REMARK 500 ASP A 43 48.1 L L OUTSIDE RANGE 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 EOH A 66 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CRN RELATED DB: PDB REMARK 900 CRAMBIN MIXED SEQUENCE ISOFORM AT 293 K REMARK 900 RELATED ID: 1AB1 RELATED DB: PDB REMARK 900 CRAMBIN PURE SER22/ILE25 ISOFORM AT 150 K REMARK 900 RELATED ID: 1CNR RELATED DB: PDB REMARK 900 CRAMBIN PURE PRO22/LEU25 ISOFORM AT 150 K REMARK 900 RELATED ID: 1CBN RELATED DB: PDB REMARK 900 CRAMBIN MIXED SEQUENCE ISOFORM AT 130 K AND 0.83 A REMARK 900 RELATED ID: 1EJG RELATED DB: PDB REMARK 900 CRAMBIN MIXED SEQUENCE ISOFORM AT 100 K AND 0.54 A REMARK 900 RELATED ID: 1JXT RELATED DB: PDB REMARK 900 1JXT IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 160 K, THE REMARK 900 SAME CRYSTAL. REMARK 900 RELATED ID: 1JXU RELATED DB: PDB REMARK 900 1JXU IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 240 K, THE REMARK 900 SAME CRYSTAL. REMARK 900 RELATED ID: 1JXW RELATED DB: PDB REMARK 900 1JXW IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 180 K, THE REMARK 900 SAME CRYSTAL. REMARK 900 RELATED ID: 1JXX RELATED DB: PDB REMARK 900 1JXX IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 200 K, THE REMARK 900 SAME CRYSTAL. REMARK 999 REMARK 999 SEQUENCE REMARK 999 PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED REMARK 999 AS ALTERNATE CONFORMERS IN COORDINATE RECORDS. REMARK 999 ONLY THE PRO22/LEU25 ISOFORM IS REPRESENTED IN THE REMARK 999 SEQUENCE RECORDS. DBREF 1JXY A 1 46 UNP P01542 CRAM_CRAAB 1 46 SEQADV 1JXY SER A 22 UNP P01542 PRO 22 MICROHETEROGENEITY SEQADV 1JXY ILE A 25 UNP P01542 LEU 25 MICROHETEROGENEITY SEQRES 1 A 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE SEQRES 2 A 46 ASN VAL CYS ARG LEU PRO GLY THR SER GLU ALA ILE CYS SEQRES 3 A 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR SEQRES 4 A 46 CYS PRO GLY ASP TYR ALA ASN HET EOH A 66 6 HETNAM EOH ETHANOL FORMUL 2 EOH C2 H6 O HELIX 1 1 SER A 6 LEU A 18 1 13 HELIX 2 2 SER A 22 GLY A 31 1 10 SHEET 1 A 2 THR A 2 CYS A 3 0 SHEET 2 A 2 ILE A 33 ILE A 34 -1 O ILE A 33 N CYS A 3 SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.05 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.05 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.06 SITE 1 AC1 2 ILE A 7 ASN A 46 CRYST1 40.880 18.560 22.410 90.00 90.67 90.00 P 1 21 1 2 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 0.024462 0.000000 0.000286 0.00000 SCALE2 0.000000 0.053879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044626 0.00000 MASTER 249 0 1 2 2 0 1 6 0 0 0 4 END