HEADER UNKNOWN FUNCTION 08-MAR-23 8IN3 TITLE EISENIA HYDROLYSIS-ENHANCING PROTEIN FROM APLYSIA KURODAI COMPND MOL_ID: 1; COMPND 2 MOLECULE: 25 KDA POLYPHENOL-BINDING PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APLYSIA KURODAI; SOURCE 3 ORGANISM_COMMON: KURODA'S SEA HARE; SOURCE 4 ORGANISM_TAXID: 6501 KEYWDS EHEP, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR X.M.SUN,Y.X.YE,K.KATO,J.YU,M.YAO REVDAT 1 15-NOV-23 8IN3 0 JRNL AUTH X.SUN,Y.YE,N.SAKURAI,H.WANG,K.KATO,J.YU,K.YUASA,A.TSUJI, JRNL AUTH 2 M.YAO JRNL TITL STRUCTURAL BASIS OF EHEP-MEDIATED OFFENSE AGAINST JRNL TITL 2 PHLOROTANNIN-INDUCED DEFENSE FROM BROWN ALGAE TO PROTECT AKU JRNL TITL 3 BGL ACTIVITY. JRNL REF ELIFE V. 12 2023 JRNL REFN ESSN 2050-084X JRNL PMID 37910430 JRNL DOI 10.7554/ELIFE.88939 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 60987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 2908 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 35.6200 - 3.1800 0.99 3157 152 0.1566 0.1593 REMARK 3 2 3.1800 - 2.5300 0.98 2993 158 0.1750 0.1736 REMARK 3 3 2.5300 - 2.2100 0.98 2950 144 0.1676 0.1779 REMARK 3 4 2.2100 - 2.0100 0.98 2915 147 0.1604 0.1749 REMARK 3 5 2.0100 - 1.8600 0.97 2879 144 0.1573 0.1737 REMARK 3 6 1.8600 - 1.7500 0.97 2885 144 0.1692 0.1752 REMARK 3 7 1.7500 - 1.6600 0.95 2820 139 0.1579 0.1819 REMARK 3 8 1.6600 - 1.5900 0.96 2824 144 0.1633 0.1658 REMARK 3 9 1.5900 - 1.5300 0.96 2830 140 0.1667 0.1830 REMARK 3 10 1.5300 - 1.4800 0.95 2794 141 0.1697 0.1944 REMARK 3 11 1.4800 - 1.4300 0.95 2779 142 0.1766 0.1640 REMARK 3 12 1.4300 - 1.3900 0.95 2780 139 0.2004 0.2252 REMARK 3 13 1.3900 - 1.3500 0.94 2766 139 0.2288 0.2431 REMARK 3 14 1.3500 - 1.3200 0.94 2743 139 0.2248 0.2302 REMARK 3 15 1.3200 - 1.2900 0.94 2744 135 0.2175 0.2187 REMARK 3 16 1.2900 - 1.2600 0.93 2726 140 0.2118 0.1852 REMARK 3 17 1.2600 - 1.2400 0.93 2726 137 0.2436 0.2508 REMARK 3 18 1.2400 - 1.2200 0.92 2691 130 0.2849 0.2807 REMARK 3 19 1.2200 - 1.1900 0.92 2685 140 0.3170 0.2952 REMARK 3 20 1.1900 - 1.1700 0.85 2476 115 0.3624 0.3686 REMARK 3 21 1.1700 - 1.1500 0.65 1916 99 0.4176 0.4117 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) : 0.137 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.022 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.04 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 : 0.005 1664 REMARK 3 ANGLE : 0.841 2288 REMARK 3 CHIRALITY : 0.081 237 REMARK 3 PLANARITY : 0.006 310 REMARK 3 DIHEDRAL : 12.727 584 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 8IN3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1300035907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60994 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M SODIUM ACETATE, 0.1 M IMIDAZOLE REMARK 280 (PH 6.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.09000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.25500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.25500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.66500 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 VAL A 2 REMARK 465 THR A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 VAL A 8 REMARK 465 SER A 9 REMARK 465 LEU A 10 REMARK 465 ALA A 11 REMARK 465 LEU A 12 REMARK 465 PHE A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 THR A 17 REMARK 465 CYS A 18 REMARK 465 GLN A 19 REMARK 465 VAL A 20 REMARK 465 GLY A 228 REMARK 465 LYS A 229 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 ASN A 216 69.50 -101.57 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 740 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 741 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 742 DISTANCE = 6.72 ANGSTROMS REMARK 525 HOH A 743 DISTANCE = 6.90 ANGSTROMS DBREF1 8IN3 A 1 229 UNP A0A1B4XTR1_APLKU DBREF2 8IN3 A A0A1B4XTR1 1 229 SEQRES 1 A 229 MET VAL THR LYS VAL LEU LEU VAL SER LEU ALA LEU PHE SEQRES 2 A 229 ALA LEU GLY THR CYS GLN VAL ALA VAL ASN LEU CYS THR SEQRES 3 A 229 GLN TYR GLY TRP PRO ASN GLY ASN TYR PRO ASP PRO TYR SEQRES 4 A 229 ASP CYS ARG LYS TYR ILE SER CYS ASN GLY ALA VAL ALA SEQRES 5 A 229 THR VAL MET SER CYS ALA LEU GLY THR VAL PHE ASN PRO SEQRES 6 A 229 ASN THR ARG ASN CYS ASP ALA TYR GLY ASN VAL PRO ILE SEQRES 7 A 229 CYS GLN TYR ALA LEU PRO SER PRO ILE VAL VAL THR ASN SEQRES 8 A 229 ILE CYS ASN GLN TYR GLY TRP GLY ASN GLY ASN PHE TYR SEQRES 9 A 229 HIS PRO TYR ASN CYS ALA GLU TYR ILE GLY CYS ALA ASN SEQRES 10 A 229 GLY LEU THR THR VAL ASN ALA CYS GLY ALA GLY GLN TYR SEQRES 11 A 229 TYR ASP GLN ALA LEU GLY ARG CYS ALA LEU ALA GLY THR SEQRES 12 A 229 GLY TYR CYS ARG GLN TYR VAL PHE THR PRO PRO PRO ALA SEQRES 13 A 229 PRO VAL VAL TYR PRO ASP GLY PHE ASP THR TYR CYS SER SEQRES 14 A 229 ALA ASN ASN LEU ALA THR GLY ILE HIS PRO ASP PRO TYR SEQRES 15 A 229 SER CYS PHE SER TYR VAL GLU CYS THR PHE GLY ARG THR SEQRES 16 A 229 THR HIS MET PRO CYS PRO ALA GLY LEU SER PHE ASP ARG SEQRES 17 A 229 SER LEU LEU VAL CYS ASP GLY ASN ARG TYR GLN ASN CYS SEQRES 18 A 229 GLY GLY ASN VAL LEU VAL GLY LYS HET GOL A 301 6 HET GOL A 302 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *343(H2 O) HELIX 1 AA1 ASN A 23 TYR A 28 1 6 HELIX 2 AA2 GLY A 74 VAL A 76 5 3 HELIX 3 AA3 ASN A 91 GLY A 97 1 7 HELIX 4 AA4 CYS A 146 VAL A 150 5 5 HELIX 5 AA5 GLY A 163 ASP A 165 5 3 HELIX 6 AA6 THR A 166 ASN A 171 1 6 HELIX 7 AA7 ASN A 216 CYS A 221 1 6 HELIX 8 AA8 GLY A 222 VAL A 227 1 6 SHEET 1 AA1 3 GLY A 33 PRO A 36 0 SHEET 2 AA1 3 LYS A 43 ASN A 48 -1 O CYS A 47 N GLY A 33 SHEET 3 AA1 3 VAL A 51 SER A 56 -1 O MET A 55 N TYR A 44 SHEET 1 AA2 2 THR A 61 ASN A 64 0 SHEET 2 AA2 2 ASN A 69 ALA A 72 -1 O ASN A 69 N ASN A 64 SHEET 1 AA3 3 GLY A 101 HIS A 105 0 SHEET 2 AA3 3 ASN A 108 ALA A 116 -1 O ILE A 113 N PHE A 103 SHEET 3 AA3 3 LEU A 119 ALA A 124 -1 O ASN A 123 N TYR A 112 SHEET 1 AA4 2 GLN A 129 ASP A 132 0 SHEET 2 AA4 2 ARG A 137 LEU A 140 -1 O ALA A 139 N TYR A 130 SHEET 1 AA5 3 GLY A 176 PRO A 179 0 SHEET 2 AA5 3 SER A 186 THR A 191 -1 O VAL A 188 N HIS A 178 SHEET 3 AA5 3 ARG A 194 PRO A 199 -1 O THR A 196 N GLU A 189 SHEET 1 AA6 2 SER A 205 ASP A 207 0 SHEET 2 AA6 2 VAL A 212 ASP A 214 -1 O VAL A 212 N ASP A 207 SSBOND 1 CYS A 25 CYS A 47 1555 1555 2.03 SSBOND 2 CYS A 41 CYS A 79 1555 1555 2.03 SSBOND 3 CYS A 57 CYS A 70 1555 1555 2.04 SSBOND 4 CYS A 93 CYS A 115 1555 1555 2.04 SSBOND 5 CYS A 109 CYS A 146 1555 1555 2.02 SSBOND 6 CYS A 125 CYS A 138 1555 1555 2.05 SSBOND 7 CYS A 168 CYS A 190 1555 1555 2.03 SSBOND 8 CYS A 184 CYS A 221 1555 1555 2.08 SSBOND 9 CYS A 200 CYS A 213 1555 1555 2.07 CISPEP 1 ALA A 156 PRO A 157 0 2.81 CRYST1 42.180 65.330 66.510 90.00 90.00 90.00 P 21 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 0.023708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015035 0.00000