HEADER ANTIMICROBIAL PROTEIN 19-DEC-21 7T9R TITLE CRYSTAL STRUCTURE OF CROCODILE DEFENSIN CPOBD13:PHOSPHATIDIC ACID TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CPOBD13; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CROCODYLUS POROSUS; SOURCE 3 ORGANISM_TAXID: 8502; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS DEFENSIN, PHOSPHATIDIC ACID, COMPLEX, PHOSPHOLIPID, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KVANSAKUL,S.WILLIAMS,M.D.HULETT REVDAT 5 13-NOV-24 7T9R 1 REMARK REVDAT 4 25-OCT-23 7T9R 1 REMARK REVDAT 3 30-AUG-23 7T9R 1 JRNL REVDAT 2 01-FEB-23 7T9R 1 SOURCE REVDAT 1 18-JAN-23 7T9R 0 JRNL AUTH S.A.WILLIAMS,F.T.LAY,G.K.BINDRA,S.BANJARA,I.K.H.POON, JRNL AUTH 2 T.K.PHAN,M.KVANSAKUL,M.D.HULETT JRNL TITL CROCODILE DEFENSIN (CPOBD13) ANTIFUNGAL ACTIVITY VIA JRNL TITL 2 PH-DEPENDENT PHOSPHOLIPID TARGETING AND MEMBRANE DISRUPTION. JRNL REF NAT COMMUN V. 14 1170 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36859344 JRNL DOI 10.1038/S41467-023-36280-Y REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874+SVN REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 21267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.310 REMARK 3 FREE R VALUE TEST SET COUNT : 916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.7800 - 2.7700 0.93 2921 128 0.1850 0.1734 REMARK 3 2 2.7700 - 2.2000 0.93 2932 146 0.1878 0.2438 REMARK 3 3 2.2000 - 1.9200 0.94 2917 157 0.1787 0.2230 REMARK 3 4 1.9200 - 1.7500 0.93 2970 106 0.1977 0.2276 REMARK 3 5 1.7500 - 1.6200 0.92 2865 138 0.2082 0.2129 REMARK 3 6 1.6200 - 1.5300 0.92 2892 108 0.2219 0.2660 REMARK 3 7 1.5300 - 1.4500 0.91 2854 133 0.2367 0.2652 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.153 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.585 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.84 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1409 REMARK 3 ANGLE : 1.064 1880 REMARK 3 CHIRALITY : 0.060 160 REMARK 3 PLANARITY : 0.004 242 REMARK 3 DIHEDRAL : 17.126 503 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7T9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000261890. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 24.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.65200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7T9Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, 0.8M POTASSIUM PHOSPHATE MONOBASIC, 0.1M SODIUM REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 350 REMARK 350 BIOMOLECULE: 4 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: D 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: 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 HE2 HIS A 35 O11 PA6 A 102 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 HIS B 12 17.98 59.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7T9Q RELATED DB: PDB REMARK 900 SAMPE PROTEIN WITHOUT LIGAND DBREF 7T9R A 1 38 PDB 7T9R 7T9R 1 38 DBREF 7T9R B 1 38 PDB 7T9R 7T9R 1 38 DBREF 7T9R C 1 38 PDB 7T9R 7T9R 1 38 DBREF 7T9R D 1 38 PDB 7T9R 7T9R 1 38 SEQRES 1 A 38 SER TYR TYR SER THR LEU GLN CYS ARG ASN ASN HIS GLY SEQRES 2 A 38 HIS CYS ARG ARG LEU CYS PHE HIS GLY GLU GLN TRP ILE SEQRES 3 A 38 GLY ASN CYS ASN GLY ARG HIS GLN HIS CYS CYS LYS SEQRES 1 B 38 SER TYR TYR SER THR LEU GLN CYS ARG ASN ASN HIS GLY SEQRES 2 B 38 HIS CYS ARG ARG LEU CYS PHE HIS GLY GLU GLN TRP ILE SEQRES 3 B 38 GLY ASN CYS ASN GLY ARG HIS GLN HIS CYS CYS LYS SEQRES 1 C 38 SER TYR TYR SER THR LEU GLN CYS ARG ASN ASN HIS GLY SEQRES 2 C 38 HIS CYS ARG ARG LEU CYS PHE HIS GLY GLU GLN TRP ILE SEQRES 3 C 38 GLY ASN CYS ASN GLY ARG HIS GLN HIS CYS CYS LYS SEQRES 1 D 38 SER TYR TYR SER THR LEU GLN CYS ARG ASN ASN HIS GLY SEQRES 2 D 38 HIS CYS ARG ARG LEU CYS PHE HIS GLY GLU GLN TRP ILE SEQRES 3 D 38 GLY ASN CYS ASN GLY ARG HIS GLN HIS CYS CYS LYS HET EDO A 101 10 HET PA6 A 102 33 HET PA6 A 103 33 HET PO4 A 104 5 HET PO4 A 105 5 HET PO4 A 106 5 HET PA6 B 201 33 HET PA6 C 101 33 HET EDO C 102 10 HET PO4 C 103 5 HET EDO D 101 10 HET PO4 D 102 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM PA6 (R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE HETNAM PO4 PHOSPHATE ION HETSYN EDO ETHYLENE GLYCOL HETSYN PA6 PHOSPHATIDIC ACID FORMUL 5 EDO 3(C2 H6 O2) FORMUL 6 PA6 4(C9 H17 O8 P) FORMUL 8 PO4 5(O4 P 3-) FORMUL 17 HOH *130(H2 O) HELIX 1 AA1 TYR A 2 ASN A 11 1 10 HELIX 2 AA2 TYR B 2 ASN B 11 1 10 HELIX 3 AA3 TYR C 2 ASN C 11 1 10 HELIX 4 AA4 TYR D 2 ASN D 11 1 10 SHEET 1 AA1 3 HIS A 14 ARG A 16 0 SHEET 2 AA1 3 HIS A 35 CYS A 37 -1 O HIS A 35 N ARG A 16 SHEET 3 AA1 3 TRP A 25 ASN A 28 -1 N GLY A 27 O CYS A 36 SHEET 1 AA2 3 HIS B 14 ARG B 16 0 SHEET 2 AA2 3 HIS B 35 CYS B 37 -1 O HIS B 35 N ARG B 16 SHEET 3 AA2 3 TRP B 25 ASN B 28 -1 N GLY B 27 O CYS B 36 SHEET 1 AA3 3 HIS C 14 ARG C 16 0 SHEET 2 AA3 3 HIS C 35 CYS C 37 -1 O HIS C 35 N ARG C 16 SHEET 3 AA3 3 TRP C 25 ASN C 28 -1 N GLY C 27 O CYS C 36 SHEET 1 AA4 3 HIS D 14 ARG D 16 0 SHEET 2 AA4 3 HIS D 35 CYS D 37 -1 O HIS D 35 N ARG D 16 SHEET 3 AA4 3 TRP D 25 ASN D 28 -1 N GLY D 27 O CYS D 36 SSBOND 1 CYS A 8 CYS A 36 1555 1555 2.01 SSBOND 2 CYS A 15 CYS A 29 1555 1555 2.02 SSBOND 3 CYS A 19 CYS A 37 1555 1555 2.00 SSBOND 4 CYS B 8 CYS B 36 1555 1555 2.03 SSBOND 5 CYS B 15 CYS B 29 1555 1555 2.02 SSBOND 6 CYS B 19 CYS B 37 1555 1555 2.02 SSBOND 7 CYS C 8 CYS C 36 1555 1555 2.02 SSBOND 8 CYS C 15 CYS C 29 1555 1555 2.02 SSBOND 9 CYS C 19 CYS C 37 1555 1555 2.03 SSBOND 10 CYS D 8 CYS D 36 1555 1555 2.03 SSBOND 11 CYS D 15 CYS D 29 1555 1555 2.02 SSBOND 12 CYS D 19 CYS D 37 1555 1555 2.01 CRYST1 27.056 33.694 36.642 90.09 90.02 90.01 P 1 4 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 0.036960 0.000009 0.000010 0.00000 SCALE2 0.000000 0.029679 0.000048 0.00000 SCALE3 0.000000 0.000000 0.027291 0.00000