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 4 16-AUG-23 1JXY 1 REMARK SEQADV 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) : 17.6 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 REMARK 3 DISCRETELY DISORDERED (MULTIPLE SUBSTATE) PROTEIN RESIDUES EACH REMARK 3 HAVE OCCUPANCY LESS THAN ONE, THEY ARE DIFFICULT TO ACCURATELY REMARK 3 REFINE. THE GEOMETRY CAN BE DISTORTED (IS POORLY DETERMINED). IN REMARK 3 THE CASE OF THR39, THE BACKBONE IS CLEARLY DISORDERED, WITH VERY REMARK 3 SMALL DEVIATIONS BETWEEN SUBSTATES (~0.1 A), AND THAT WAS NOT REMARK 3 INCLUDED IN THE MODEL. HENCE THERE MAY BE LARGE ERRORS INVOLVING REMARK 3 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 DEPOSITION ID IS D_1000014314. 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 : TEXSAN, 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 2 CA THR A 2 CB 0.170 REMARK 500 VAL A 8 N VAL A 8 CA 0.160 REMARK 500 VAL A 8 CA VAL A 8 C -0.174 REMARK 500 SER A 22 CB SER A 22 OG 0.113 REMARK 500 SER A 22 CB SER A 22 OG -0.240 REMARK 500 LEU A 25 CG LEU A 25 CD2 0.303 REMARK 500 THR A 30 N THR A 30 CA 0.171 REMARK 500 THR A 30 CA THR A 30 CB 0.173 REMARK 500 THR A 30 CA THR A 30 C -0.197 REMARK 500 ILE A 34 CB ILE A 34 CG1 0.320 REMARK 500 THR A 39 CA THR A 39 CB 0.159 REMARK 500 THR A 39 CA THR A 39 C 0.284 REMARK 500 ASP A 43 N ASP A 43 CA 0.183 REMARK 500 ASP A 43 CA ASP A 43 CB 0.234 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 2 CA - CB - CG2 ANGL. DEV. = -12.6 DEGREES REMARK 500 VAL A 8 CB - CA - C ANGL. DEV. = 22.6 DEGREES REMARK 500 SER A 22 N - CA - CB ANGL. DEV. = -12.6 DEGREES REMARK 500 SER A 22 CA - CB - OG ANGL. DEV. = -18.0 DEGREES REMARK 500 LEU A 25 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 THR A 30 CB - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 THR A 30 N - CA - CB ANGL. DEV. = -12.5 DEGREES REMARK 500 THR A 30 CA - CB - OG1 ANGL. DEV. = -13.8 DEGREES REMARK 500 THR A 30 CA - CB - CG2 ANGL. DEV. = 12.7 DEGREES REMARK 500 THR A 39 C - N - CA ANGL. DEV. = -21.4 DEGREES REMARK 500 THR A 39 N - CA - CB ANGL. DEV. = -15.1 DEGREES REMARK 500 THR A 39 CA - CB - CG2 ANGL. DEV. = -12.5 DEGREES REMARK 500 THR A 39 CA - C - O ANGL. DEV. = 14.4 DEGREES REMARK 500 THR A 39 CA - C - N ANGL. DEV. = -17.4 DEGREES REMARK 500 ASP A 43 N - CA - CB ANGL. DEV. = -21.1 DEGREES REMARK 500 ASP A 43 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES 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 SAME REMARK 900 CRYSTAL. REMARK 900 RELATED ID: 1JXU RELATED DB: PDB REMARK 900 1JXU IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 240 K, THE SAME REMARK 900 CRYSTAL. REMARK 900 RELATED ID: 1JXW RELATED DB: PDB REMARK 900 1JXW IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 180 K, THE SAME REMARK 900 CRYSTAL. REMARK 900 RELATED ID: 1JXX RELATED DB: PDB REMARK 900 1JXX IS MIXED SEQUENCE ISOFORM OF CRAMBIN AT 200 K, THE SAME REMARK 900 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