HEADER PLANT PROTEIN 11-JUL-25 9PIS TITLE AB INITIO STRUCTURE OF CRAMBIN BY MICROED AT 0.85A 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_COMMON: ABYSSINIAN CRAMBE; SOURCE 4 ORGANISM_TAXID: 3721; SOURCE 5 STRAIN: MEYER KEYWDS SEED PROTEIN, PLANT PROTEIN EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR P.C.R.VASIREDDY,T.LOW-BEER,K.A.SPOTH,D.ACEHAN,M.R.CRAWLEY, AUTHOR 2 M.W.MARTYNOWYCZ REVDAT 1 25-FEB-26 9PIS 0 JRNL AUTH P.C.R.VASIREDDY,T.LOW-BEER,K.A.SPOTH,D.ACEHAN,M.R.CRAWLEY, JRNL AUTH 2 M.W.MARTYNOWYCZ JRNL TITL DIRECT FROM THE SEED: AN ATOMIC RESOLUTION PROTEIN STRUCTURE JRNL TITL 2 BY AB INITIO MICROED. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41690942 JRNL DOI 10.1038/S41467-026-69601-Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.C.R.VASIREDDY,T.LOW-BEER,K.A.SPOTH,D.ACEHAN,M.R.CRAWLEY, REMARK 1 AUTH 2 M.W.MARTYNOWYCZ REMARK 1 TITL DIRECT FROM THE SEED: AN ATOMIC-RESOLUTION PROTEIN STRUCTURE REMARK 1 TITL 2 BY AB INITIO MICROED REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 DOI 10.1101/2025.07.03.663097 REMARK 2 REMARK 2 RESOLUTION. 0.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 72.0 REMARK 3 NUMBER OF REFLECTIONS : 22251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM SELECTION REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.137 REMARK 3 FREE R VALUE TEST SET COUNT : 1143 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) : 0.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.87 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 10.89 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 235 REMARK 3 BIN R VALUE (WORKING SET) : 0.4440 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 12 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 : 325 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60000 REMARK 3 B22 (A**2) : 1.41200 REMARK 3 B33 (A**2) : -0.81300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.30000 REMARK 3 B23 (A**2) : 0.00000 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9PIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000297923. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : TFS GLACIOS REMARK 240 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL 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 9.39500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 170 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 171 DISTANCE = 6.54 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9Z6F RELATED DB: PDB REMARK 900 X-RAY STRUCRTURE OF CRAMBIN FROM SAME SOURCE DBREF 9PIS A 1 46 UNP P01542 CRAM_CRAAB 1 46 SEQADV 9PIS SER A 22 UNP P01542 PRO 22 VARIANT SEQADV 9PIS ILE A 25 UNP P01542 LEU 25 VARIANT 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 FORMUL 2 HOH *71(H2 O) HELIX 1 AA1 SER A 6 LEU A 18 1 13 HELIX 2 AA2 SER A 22 GLY A 31 1 10 SHEET 1 AA1 2 THR A 2 CYS A 3 0 SHEET 2 AA1 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 2.04 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.11 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.12 CRYST1 41.490 18.790 22.520 90.00 90.84 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 0.024102 0.000000 0.000351 0.00000 SCALE2 0.000000 0.053220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044410 0.00000 CONECT 46 625 CONECT 56 494 CONECT 251 401 CONECT 401 251 CONECT 494 56 CONECT 625 46 MASTER 193 0 0 2 2 0 0 6 396 1 6 4 END