HEADER PLANT PROTEIN 29-SEP-21 7PUD TITLE BRYOPORIN - ACTINOPORIN FROM MOSS PHYSCOMITRIUM PATENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRYOPORIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPBP,PHYSCOMITRIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSCOMITRIUM PATENS; SOURCE 3 ORGANISM_COMMON: SPREADING-LEAVED EARTH MOSS, PHYSCOMITRELLA PATENS; SOURCE 4 ORGANISM_TAXID: 3218; SOURCE 5 GENE: PHYPADRAFT_61094; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS ACTINOPORIN, MEMBRANE-BINDING, PORE-FORMATION, MOSS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.SOLINC,G.ANDERLUH,M.PODOBNIK REVDAT 4 31-JAN-24 7PUD 1 REMARK REVDAT 3 12-OCT-22 7PUD 1 JRNL REVDAT 2 05-OCT-22 7PUD 1 JRNL REVDAT 1 28-SEP-22 7PUD 0 JRNL AUTH G.SOLINC,T.SVIGELJ,N.OMERSA,T.SNOJ,K.PIRC,N.ZNIDARSIC, JRNL AUTH 2 A.YAMAJI-HASEGAWA,T.KOBAYASHI,G.ANDERLUH,M.PODOBNIK JRNL TITL PORE-FORMING MOSS PROTEIN BRYOPORIN IS STRUCTURALLY AND JRNL TITL 2 MECHANISTICALLY RELATED TO ACTINOPORINS FROM EVOLUTIONARILY JRNL TITL 3 DISTANT CNIDARIANS. JRNL REF J.BIOL.CHEM. V. 298 02455 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36063994 JRNL DOI 10.1016/J.JBC.2022.102455 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 44629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1965 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 32.7500 - 3.0100 0.99 3435 158 0.1767 0.1866 REMARK 3 2 3.0100 - 2.3900 1.00 3322 154 0.1847 0.2166 REMARK 3 3 2.3900 - 2.0900 0.95 3154 144 0.2144 0.2337 REMARK 3 4 2.0900 - 1.9000 0.93 3019 136 0.2312 0.2354 REMARK 3 5 1.9000 - 1.7600 0.99 3262 151 0.1918 0.2100 REMARK 3 6 1.7600 - 1.6600 1.00 3216 149 0.1812 0.2132 REMARK 3 7 1.6600 - 1.5800 1.00 3220 149 0.1725 0.1878 REMARK 3 8 1.5800 - 1.5100 0.99 3195 147 0.1874 0.2303 REMARK 3 9 1.5100 - 1.4500 0.87 2819 128 0.3363 0.2949 REMARK 3 10 1.4500 - 1.4000 0.91 2937 136 0.2510 0.3076 REMARK 3 11 1.4000 - 1.3600 0.98 3112 144 0.1891 0.2438 REMARK 3 12 1.3600 - 1.3200 0.95 3076 142 0.2376 0.2531 REMARK 3 13 1.3200 - 1.2800 0.66 2120 99 0.5365 0.5390 REMARK 3 14 1.2800 - 1.2500 0.87 2777 128 0.2873 0.3409 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.67 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 : 0.007 1544 REMARK 3 ANGLE : 0.946 2116 REMARK 3 CHIRALITY : 0.092 220 REMARK 3 PLANARITY : 0.006 270 REMARK 3 DIHEDRAL : 10.664 217 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 7PUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : A VERTICAL COLLIMATING MIRROR, A REMARK 200 DOUBLE-CRYSTAL SI(111) REMARK 200 MONOCHROMATOR, A BENDABLE REMARK 200 FOCUSSING MIRROR REMARK 200 OPTICS : A VERTICAL COLLIMATING MIRROR, A REMARK 200 DOUBLE-CRYSTAL SI(111) REMARK 200 MONOCHROMATOR, A BENDABLE REMARK 200 FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45262 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 34.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04733 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41680 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.18.2_3874 REMARK 200 STARTING MODEL: 3VWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, NACL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.24850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.98350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.24850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.98350 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 179 REMARK 465 LEU A 180 REMARK 465 ALA A 181 REMARK 465 ALA A 182 REMARK 465 ALA A 183 REMARK 465 LEU A 184 REMARK 465 GLU A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 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 ALA A 79 42.91 -91.74 REMARK 500 ASP A 92 -6.46 92.48 REMARK 500 ASN A 166 -167.72 -121.99 REMARK 500 GLN A 168 66.99 -117.91 REMARK 500 REMARK 500 REMARK: NULL 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 479 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 480 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 481 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 6.67 ANGSTROMS DBREF 7PUD A 1 178 UNP Q5UCA8 BRYP_PHYPA 1 178 SEQADV 7PUD LYS A 179 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD LEU A 180 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD ALA A 181 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD ALA A 182 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD ALA A 183 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD LEU A 184 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD GLU A 185 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 186 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 187 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 188 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 189 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 190 UNP Q5UCA8 EXPRESSION TAG SEQADV 7PUD HIS A 191 UNP Q5UCA8 EXPRESSION TAG SEQRES 1 A 191 MET ALA GLU ALA ILE ILE PRO ALA ALA GLU LEU SER ILE SEQRES 2 A 191 LYS THR LEU GLN ASN ILE VAL GLU GLY ILE THR GLY VAL SEQRES 3 A 191 ASP ARG LYS ILE ALA ILE GLY PHE LYS ASN LEU THR ASP SEQRES 4 A 191 TYR THR LEU GLU ASN LEU GLY VAL TYR PHE ASN SER GLY SEQRES 5 A 191 SER SER ASP ARG SER ILE ALA TYR LYS ILE ASN ALA GLN SEQRES 6 A 191 GLU ALA LEU LEU PHE SER ALA ARG LYS SER ASP HIS THR SEQRES 7 A 191 ALA ARG GLY THR VAL GLY THR PHE SER TYR TYR ILE GLN SEQRES 8 A 191 ASP GLU ASP LYS THR VAL HIS VAL MET TRP SER VAL PRO SEQRES 9 A 191 PHE ASP TYR ASN LEU TYR SER ASN TRP TRP ASN ILE ALA SEQRES 10 A 191 VAL VAL ASP GLY ARG GLN PRO PRO ASP SER ASN VAL HIS SEQRES 11 A 191 ASP ASN LEU TYR ASN GLY SER GLY GLY MET PRO TYR PRO SEQRES 12 A 191 ASN LYS PRO ASP GLN TYR ILE ASN ASN GLU GLN LYS GLY SEQRES 13 A 191 PHE HIS LEU PHE GLY SER MET THR ASN ASN GLY GLN ALA SEQRES 14 A 191 THR ILE GLU VAL GLU LEU LYS LYS ALA LYS LEU ALA ALA SEQRES 15 A 191 ALA LEU GLU HIS HIS HIS HIS HIS HIS HET MPD A 201 8 HET MPD A 202 8 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET SO4 A 207 5 HET SO4 A 208 5 HET SO4 A 209 5 HET SO4 A 210 5 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION FORMUL 2 MPD 2(C6 H14 O2) FORMUL 4 SO4 8(O4 S 2-) FORMUL 12 HOH *182(H2 O) HELIX 1 AA1 ALA A 9 LEU A 11 5 3 HELIX 2 AA2 SER A 12 GLY A 22 1 11 HELIX 3 AA3 ASP A 126 GLY A 136 1 11 SHEET 1 AA1 6 ILE A 5 PRO A 7 0 SHEET 2 AA1 6 GLU A 66 ARG A 73 -1 O ALA A 67 N ILE A 6 SHEET 3 AA1 6 LYS A 29 ASN A 36 -1 N ASN A 36 O GLU A 66 SHEET 4 AA1 6 GLN A 168 LYS A 177 1 O ILE A 171 N GLY A 33 SHEET 5 AA1 6 PHE A 157 MET A 163 -1 N HIS A 158 O LYS A 176 SHEET 6 AA1 6 ILE A 150 GLN A 154 -1 N ILE A 150 O GLY A 161 SHEET 1 AA2 5 LYS A 61 ILE A 62 0 SHEET 2 AA2 5 LEU A 42 SER A 51 -1 N LEU A 42 O ILE A 62 SHEET 3 AA2 5 THR A 82 ILE A 90 -1 O TYR A 89 N GLU A 43 SHEET 4 AA2 5 LYS A 95 VAL A 103 -1 O LYS A 95 N ILE A 90 SHEET 5 AA2 5 TRP A 113 ASP A 120 -1 O VAL A 119 N THR A 96 CRYST1 37.918 54.497 81.967 90.00 90.00 90.00 P 2 21 21 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 0.026373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012200 0.00000