HEADER PEPTIDE BINDING PROTEIN 23-APR-24 9F2M TITLE TO BE PUBLISHED COMPND MOL_ID: 1; COMPND 2 MOLECULE: AUTOPHAGY-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N- AND C-TERMINAL TRUNCATED VARIANT; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RXLR EFFECTOR PROTEIN 54; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PEPTIDE FROM IRISH POTATO FAMINE PATHOGEN EFFECTOR COMPND 11 PROTEIN PEXRD54 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARCHANTIA POLYMORPHA; SOURCE 3 ORGANISM_COMMON: LIVERWORT; SOURCE 4 ORGANISM_TAXID: 3197; SOURCE 5 GENE: MARPO_0001S0494; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: PHYTOPHTHORA INFESTANS; SOURCE 11 ORGANISM_COMMON: POTATO LATE BLIGHT AGENT; SOURCE 12 ORGANISM_TAXID: 4787 KEYWDS SIGNALING PROTEIN AUTOPHAGY RELATED PROTEIN, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.SANCHEZ DE MEDINA,Y.DAGDAS REVDAT 1 21-MAY-25 9F2M 0 JRNL AUTH N.NN,P.PP JRNL TITL TO BE PUBLISHED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 10218 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) : 0.192 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 511 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 28.6000 - 2.7700 0.96 2363 125 0.1635 0.2107 REMARK 3 2 2.7700 - 2.2000 1.00 2488 131 0.2289 0.2812 REMARK 3 3 2.2000 - 1.9200 0.99 2409 127 0.2191 0.2548 REMARK 3 4 1.9200 - 1.7500 1.00 2447 128 0.2542 0.3354 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) : 0.255 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.05 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 : 0.015 991 REMARK 3 ANGLE : 1.364 1344 REMARK 3 CHIRALITY : 0.094 148 REMARK 3 PLANARITY : 0.015 172 REMARK 3 DIHEDRAL : 13.879 392 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 57 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3263 -2.1445 -25.9441 REMARK 3 T TENSOR REMARK 3 T11: 0.2251 T22: 0.3655 REMARK 3 T33: 0.2756 T12: 0.0002 REMARK 3 T13: -0.0790 T23: -0.0348 REMARK 3 L TENSOR REMARK 3 L11: 1.6082 L22: 3.8622 REMARK 3 L33: 3.7338 L12: -0.2091 REMARK 3 L13: -1.3851 L23: 0.1347 REMARK 3 S TENSOR REMARK 3 S11: 0.1375 S12: 0.2997 S13: -0.2732 REMARK 3 S21: -0.0351 S22: -0.2348 S23: 0.0603 REMARK 3 S31: 0.1299 S32: 0.0576 S33: 0.0948 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 58 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.6513 6.6449 -17.5519 REMARK 3 T TENSOR REMARK 3 T11: 0.2821 T22: 0.2351 REMARK 3 T33: 0.2072 T12: -0.0386 REMARK 3 T13: 0.0054 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 3.9541 L22: 2.1813 REMARK 3 L33: 3.3717 L12: 0.0270 REMARK 3 L13: 0.2740 L23: 0.6529 REMARK 3 S TENSOR REMARK 3 S11: 0.1154 S12: 0.2398 S13: 0.1201 REMARK 3 S21: 0.0843 S22: -0.1936 S23: 0.1504 REMARK 3 S31: -0.4214 S32: 0.0471 S33: 0.0892 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4728 -1.4670 -17.5060 REMARK 3 T TENSOR REMARK 3 T11: 0.2566 T22: 0.3580 REMARK 3 T33: 0.3175 T12: -0.0500 REMARK 3 T13: -0.0697 T23: 0.0437 REMARK 3 L TENSOR REMARK 3 L11: 2.0378 L22: 4.0845 REMARK 3 L33: 2.1488 L12: 0.0208 REMARK 3 L13: -0.4951 L23: -0.2815 REMARK 3 S TENSOR REMARK 3 S11: 0.2625 S12: -0.2744 S13: -0.2719 REMARK 3 S21: 0.4078 S22: -0.2151 S23: -0.1714 REMARK 3 S31: 0.0138 S32: 0.3588 S33: -0.0179 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.2110 4.8291 -31.6310 REMARK 3 T TENSOR REMARK 3 T11: 0.3685 T22: 0.5011 REMARK 3 T33: 0.2442 T12: -0.0604 REMARK 3 T13: 0.0438 T23: 0.0620 REMARK 3 L TENSOR REMARK 3 L11: 5.6617 L22: 3.3878 REMARK 3 L33: 6.2196 L12: 0.8557 REMARK 3 L13: 1.2748 L23: 4.5720 REMARK 3 S TENSOR REMARK 3 S11: 0.4686 S12: 0.8502 S13: -0.2897 REMARK 3 S21: -0.6764 S22: 0.0161 S23: -0.4179 REMARK 3 S31: 0.1264 S32: -0.9411 S33: -0.6116 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 9F2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292138037. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1500, 100 MM PCTP REMARK 280 (SODIUM PROPIONIC ACID, SODIUM CACODYLATE, BIS-TRIS PROPANE) PH REMARK 280 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.39333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.19667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 DBREF1 9F2M A 5 113 UNP A0A2R6XWU1_MARPO DBREF2 9F2M A A0A2R6XWU1 7 115 DBREF 9F2M D 1 5 UNP D0NBE6 RD54_PHYIT 377 381 SEQRES 1 A 109 SER PHE LYS LYS GLU HIS PRO LEU GLU LYS ARG GLN ALA SEQRES 2 A 109 GLU ALA SER ARG ILE ARG ASN LYS TYR PRO ASP ARG ILE SEQRES 3 A 109 PRO VAL ILE VAL GLU ARG ALA GLU LYS SER ASP ILE PRO SEQRES 4 A 109 ASP ILE ASP LYS LYS LYS TYR LEU VAL PRO ALA ASP LEU SEQRES 5 A 109 THR VAL GLY GLN PHE VAL PHE VAL ILE ARG LYS ARG ILE SEQRES 6 A 109 LYS LEU SER ALA GLU LYS ALA ILE PHE ILE PHE VAL ARG SEQRES 7 A 109 ASN VAL LEU PRO PRO THR ALA ALA MET MET SER ALA ILE SEQRES 8 A 109 TYR ASP GLU HIS LYS ASP ASP ASP GLY PHE LEU TYR LEU SEQRES 9 A 109 THR TYR SER GLY GLU SEQRES 1 D 5 ASP TRP GLU ILE VAL FORMUL 3 HOH *91(H2 O) HELIX 1 AA1 SER A 5 HIS A 10 1 6 HELIX 2 AA2 PRO A 11 TYR A 26 1 16 HELIX 3 AA3 THR A 57 LYS A 70 1 14 HELIX 4 AA4 MET A 91 LYS A 100 1 10 SHEET 1 AA1 5 PHE A 78 PHE A 80 0 SHEET 2 AA1 5 LEU A 106 SER A 111 -1 O SER A 111 N PHE A 78 SHEET 3 AA1 5 ARG A 29 ARG A 36 1 N ILE A 33 O LEU A 108 SHEET 4 AA1 5 LYS A 49 PRO A 53 -1 O VAL A 52 N ILE A 30 SHEET 5 AA1 5 GLU D 3 ILE D 4 1 O GLU D 3 N LEU A 51 CRYST1 36.230 36.230 69.590 90.00 90.00 120.00 P 32 3 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 0.027601 0.015936 0.000000 0.00000 SCALE2 0.000000 0.031871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014370 0.00000 MASTER 252 0 0 4 5 0 0 6 1029 2 0 10 END