PDB Short entry for 1EJG HEADER PLANT PROTEIN 02-MAR-00 1EJG TITLE CRAMBIN AT ULTRA-HIGH RESOLUTION: VALENCE ELECTRON DENSITY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRAMBIN (PRO22,SER22/LEU25,ILE25); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CRAMBIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA; SOURCE 3 ORGANISM_TAXID: 3721; SOURCE 4 STRAIN: SUBSP. ABYSSINICA KEYWDS VALENCE ELECTRON DENSITY, MULTI-SUBSTATE, MULTIPOLE REFINEMENT, PLANT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.JELSCH,M.M.TEETER,V.LAMZIN,V.PICHON-LESME,B.BLESSING,C.LECOMTE REVDAT 7 04-OCT-17 1EJG 1 REMARK REVDAT 6 05-FEB-14 1EJG 1 ATOM CONECT REVDAT 5 13-JUL-11 1EJG 1 VERSN REVDAT 4 24-FEB-09 1EJG 1 VERSN REVDAT 3 01-APR-03 1EJG 1 JRNL REVDAT 2 10-MAY-00 1EJG 1 COMPND ATOM REVDAT 1 05-APR-00 1EJG 0 JRNL AUTH C.JELSCH,M.M.TEETER,V.LAMZIN,V.PICHON-PESME,R.H.BLESSING, JRNL AUTH 2 C.LECOMTE JRNL TITL ACCURATE PROTEIN CRYSTALLOGRAPHY AT ULTRA-HIGH RESOLUTION: JRNL TITL 2 VALENCE ELECTRON DISTRIBUTION IN CRAMBIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 3171 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 10737790 JRNL DOI 10.1073/PNAS.97.7.3171 REMARK 2 REMARK 2 RESOLUTION. 0.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MOLLY REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 100989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 1 REFLECTION OUT OF 20 REMARK 3 R VALUE (WORKING SET) : 0.090 REMARK 3 FREE R VALUE : 0.094 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 11220 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.57 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 17547 REMARK 3 BIN R VALUE (WORKING SET) : 0.1970 REMARK 3 BIN FREE R VALUE : 0.2050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 340 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 2.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.023 REMARK 3 BOND ANGLES (DEGREES) : 2.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : SHELXL97 DICTIONARY REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SHELX97 FOLLOWED BY MOLLY (N.K.HANSEN & REMARK 3 P.COPPENS ACTA CRYSTALLOGR. A34, 909-921) REFINEMENT OF ELECTRON REMARK 3 DENSITY. REMARK 4 REMARK 4 1EJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7 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) : 0.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DREAR REMARK 200 DATA SCALING SOFTWARE : DREAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79868 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.540 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.14760 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: NULL REMARK 200 SOFTWARE USED: ALREADY SOLVED REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL 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: THE PROTEIN (40 MG/ML IN 80% ETHANOL) REMARK 280 IS EQUILIBRATED AGAINST 60% ETHANOL. NOT BUFFERED., PH 7, VAPOR REMARK 280 DIFFUSION, 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 9.24900 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 22 N REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N PRO A 22 CA SER A 22 1.39 REMARK 500 N PRO A 22 CA SER A 22 1.60 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 1 CA - CB - OG1 ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 SER A 22 CA - C - O ANGL. DEV. = 14.1 DEGREES REMARK 500 SER A 22 O - C - N ANGL. DEV. = -13.1 DEGREES REMARK 500 TYR A 29 CB - CG - CD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 TYR A 29 CB - CG - CD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 TYR A 29 CG - CD1 - CE1 ANGL. DEV. = 5.7 DEGREES REMARK 500 THR A 39 CA - CB - CG2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ASP A 43 CA - CB - CG ANGL. DEV. = 13.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 22 -10.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CBN RELATED DB: PDB REMARK 900 CRAMBIN AT 130K AND 0.83 A. TWO SEQUENCE FORMS. REMARK 900 RELATED ID: 1CRN RELATED DB: PDB REMARK 900 CRAMBIN AT 1.5 A AND ROOM TEMPERATURE. TWO SEQUENCE FORMS. REMARK 900 RELATED ID: 1AB1 RELATED DB: PDB REMARK 900 CRAMBIN AT 150 K IN THE PURE SER22/ILE25 SEQUENCE FORMS. REMARK 900 RELATED ID: 1CNR RELATED DB: PDB REMARK 900 CRAMBIN AT 150K AND 1.05 A RESOLUTION. PURE PRO22/LEU25 FORM OF REMARK 900 CRAMBIN. DBREF 1EJG A 1 46 UNP P01542 CRAM_CRAAB 1 46 SEQADV 1EJG SER A 22 UNP P01542 PRO 22 MICROHETEROGENEITY SEQADV 1EJG 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 PRO GLU ALA LEU 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 HELIX 1 1 SER A 6 LEU A 18 1 13 HELIX 2 2 PRO 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 2.03 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.05 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.04 CRYST1 40.824 18.498 22.371 90.00 90.47 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 0.024495 0.000000 0.000201 0.00000 SCALE2 0.000000 0.054060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044702 0.00000