HEADER ANTIFUNGAL PROTEIN 16-OCT-23 8ULM TITLE CHICKPEA (CICER ARIENTINUM) NODULE-SPECIFIC CYSTEINE-RICH PEPTIDE TITLE 2 NCR13: SOLUTION NMR STRUCTURE OF THE ISOMER WITH C4:C23, C15:C30, AND TITLE 3 C10:C28 DISULFIDE BONDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NODULE CYSTEINE-RICH PROTEIN 13; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CICER ARIETINUM; SOURCE 3 ORGANISM_COMMON: CHICKPEA; SOURCE 4 ORGANISM_TAXID: 3827; SOURCE 5 GENE: NCR13; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS ANTIFUNAL ACTIVITY, ENDOSYMBIOTIC, DISULFIDE-RICH, ANTIMICROBIAL KEYWDS 2 PROTEIN, NCR PEPTIDE, ANTIFUNGAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.W.BUCHKO,M.ZHOU,D.M.SHAH,S.L.S.VELIVELLI REVDAT 1 01-NOV-23 8ULM 0 JRNL AUTH G.W.BUCHKO,M.ZHOU,S.L.S.VELIVELLI,D.M.SHAH JRNL TITL SOLUTION NMR STRUCTURES OF THE CHICKPEA (CICER ARIENTINUM) JRNL TITL 2 NODULE-SPECIFIC CYSTEINE-RICH PEPTIDE NCR13 IN TWO DIFFERENT JRNL TITL 3 DISULFIDE BONDING PATTERNS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IT WAS NOT POSSIBLE TO VERIFY THE REMARK 3 DISULFIDE BONDING PATTERN USING MASS SPECTROMETRY OR OTHER REMARK 3 METHODS. THEREFORE THE ALPHAFOLD PREDICTED DISULFIDE PATTERN WAS REMARK 3 USED IN THE STRUCTURE CALCULATIONS. THE STRUCTURE WAS FIRST REMARK 3 SOLVED USING CYANA AND THEN REFINED IN EXPLICIT WATER ADDING 10% REMARK 3 TO THE UPPER BOUND OF THE NOE RESTRAINTS. REMARK 4 REMARK 4 8ULM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278334. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.3 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM ACETATE, 50 MM REMARK 210 SODIUM CHLORIDE, 93% H2O/7% D2O; REMARK 210 20 MM SODIUM ACETATE, 50 MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H TOCSY; 3D 1H-15N TOCSY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2007, CYANA 2.1, POKY, REMARK 210 PSVS 3.135, TALOS+ REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 PRO A 3 -160.19 -67.07 REMARK 500 1 PHE A 13 98.08 -38.83 REMARK 500 1 LYS A 19 142.96 -176.02 REMARK 500 2 PRO A 3 -165.50 -71.51 REMARK 500 2 GLN A 5 65.92 65.93 REMARK 500 2 PHE A 13 99.16 -38.96 REMARK 500 3 PRO A 3 -159.67 -73.89 REMARK 500 3 PHE A 13 98.91 -38.37 REMARK 500 3 ARG A 16 98.84 -63.16 REMARK 500 3 LYS A 19 143.82 -172.86 REMARK 500 4 PRO A 3 -167.44 -78.73 REMARK 500 4 PHE A 13 97.62 -38.61 REMARK 500 4 LYS A 19 130.68 -174.16 REMARK 500 5 GLN A 5 30.06 72.32 REMARK 500 5 PHE A 13 98.30 -38.88 REMARK 500 6 PRO A 3 -163.12 -77.93 REMARK 500 6 PHE A 13 98.20 -38.55 REMARK 500 6 LYS A 19 145.58 -172.68 REMARK 500 7 PRO A 3 -163.32 -69.90 REMARK 500 7 PHE A 13 98.05 -39.22 REMARK 500 7 LYS A 19 122.13 -179.83 REMARK 500 8 PRO A 3 -160.83 -62.75 REMARK 500 8 GLN A 5 67.27 62.12 REMARK 500 8 PHE A 13 98.07 -38.99 REMARK 500 9 PRO A 3 -171.41 -65.72 REMARK 500 9 GLN A 5 66.90 68.38 REMARK 500 9 PHE A 13 98.12 -38.80 REMARK 500 9 ARG A 16 96.19 -64.56 REMARK 500 9 LYS A 19 149.73 -176.89 REMARK 500 10 PRO A 3 -157.96 -72.55 REMARK 500 10 GLN A 5 41.69 73.79 REMARK 500 10 PHE A 13 98.78 -39.29 REMARK 500 10 ARG A 16 96.10 -65.07 REMARK 500 10 LYS A 19 139.87 178.56 REMARK 500 11 PHE A 13 98.37 -38.92 REMARK 500 11 ARG A 16 96.70 -66.78 REMARK 500 11 LYS A 19 127.44 177.82 REMARK 500 12 PRO A 3 -161.75 -76.35 REMARK 500 12 PHE A 13 98.61 -39.11 REMARK 500 12 LYS A 19 142.69 -175.56 REMARK 500 13 THR A 1 -83.16 -73.64 REMARK 500 13 LYS A 2 88.94 -156.42 REMARK 500 13 PRO A 3 -174.41 -59.48 REMARK 500 13 GLN A 5 65.96 67.69 REMARK 500 13 PHE A 13 97.74 -38.98 REMARK 500 14 PRO A 3 179.10 -52.84 REMARK 500 14 GLN A 5 63.03 63.65 REMARK 500 14 PHE A 13 98.79 -38.84 REMARK 500 14 ARG A 16 99.76 -64.43 REMARK 500 14 LYS A 19 133.09 -170.55 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 12 PHE A 13 6 -149.30 REMARK 500 LYS A 12 PHE A 13 9 -148.25 REMARK 500 LYS A 12 PHE A 13 14 -149.69 REMARK 500 LYS A 12 PHE A 13 16 -145.97 REMARK 500 LYS A 12 PHE A 13 18 -146.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7TH8 RELATED DB: PDB REMARK 900 DIFFERENT DISULFIDE BOND PATTERN REMARK 900 RELATED ID: 31111 RELATED DB: BMRB REMARK 900 CHICKPEA (CICER ARIENTINUM) NODULE-SPECIFIC CYSTEINE-RICH PEPTIDE REMARK 900 NCR13: SOLUTION NMR STRUCTURE OF THE ISOMER WITH C4:C23, C15:C30, REMARK 900 AND C10:C28 DISULFIDE BONDS DBREF1 8ULM A 0 32 UNP A0A0U8SNQ0_CICAR DBREF2 8ULM A A0A0U8SNQ0 24 56 SEQRES 1 A 33 ALA THR LYS PRO CYS GLN SER ASP LYS ASP CYS LYS LYS SEQRES 2 A 33 PHE ALA CYS ARG LYS PRO LYS VAL PRO LYS CYS ILE ASN SEQRES 3 A 33 GLY PHE CYS LYS CYS VAL ARG HELIX 1 AA1 GLN A 5 CYS A 10 1 6 SHEET 1 AA1 2 VAL A 20 ILE A 24 0 SHEET 2 AA1 2 PHE A 27 VAL A 31 -1 O LYS A 29 N LYS A 22 SSBOND 1 CYS A 4 CYS A 23 1555 1555 2.23 SSBOND 2 CYS A 10 CYS A 28 1555 1555 2.23 SSBOND 3 CYS A 15 CYS A 30 1555 1555 2.23 CISPEP 1 LYS A 17 PRO A 18 1 -3.37 CISPEP 2 LYS A 17 PRO A 18 2 1.91 CISPEP 3 LYS A 17 PRO A 18 3 0.51 CISPEP 4 LYS A 17 PRO A 18 4 0.61 CISPEP 5 LYS A 17 PRO A 18 5 1.87 CISPEP 6 LYS A 17 PRO A 18 6 1.19 CISPEP 7 LYS A 17 PRO A 18 7 1.77 CISPEP 8 LYS A 17 PRO A 18 8 1.47 CISPEP 9 LYS A 17 PRO A 18 9 3.79 CISPEP 10 LYS A 17 PRO A 18 10 3.73 CISPEP 11 LYS A 17 PRO A 18 11 4.89 CISPEP 12 LYS A 17 PRO A 18 12 0.62 CISPEP 13 LYS A 17 PRO A 18 13 1.44 CISPEP 14 LYS A 17 PRO A 18 14 0.11 CISPEP 15 LYS A 17 PRO A 18 15 -2.29 CISPEP 16 LYS A 17 PRO A 18 16 2.31 CISPEP 17 LYS A 17 PRO A 18 17 -1.34 CISPEP 18 LYS A 17 PRO A 18 18 4.58 CISPEP 19 LYS A 17 PRO A 18 19 3.23 CISPEP 20 LYS A 17 PRO A 18 20 1.94 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1