HEADER HYDROLASE INHIBITOR 14-SEP-22 8EHD TITLE STRUCTURE OF TANNERELLA FORSYTHIA POTEMPIN E COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTEMPIN E (POTE); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TANNERELLA FORSYTHIA; SOURCE 3 ORGANISM_TAXID: 28112; SOURCE 4 GENE: TFUB20_00705; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOPEPTIDASE INHIBITOR, HYDROLASE, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR F.X.GOMIS-RUTH REVDAT 3 25-OCT-23 8EHD 1 REMARK REVDAT 2 22-FEB-23 8EHD 1 JRNL REVDAT 1 21-DEC-22 8EHD 0 JRNL AUTH M.KSIAZEK,T.GOULAS,D.MIZGALSKA,A.RODRIGUEZ-BANQUERI, JRNL AUTH 2 U.ECKHARD,F.VEILLARD,I.WALIGORSKA,M.BENEDYK-MACHACZKA, JRNL AUTH 3 A.M.SOCHAJ-GREGORCZYK,M.MADEJ,I.B.THOGERSEN,J.J.ENGHILD, JRNL AUTH 4 A.CUPPARI,J.L.AROLAS,I.DE DIEGO,M.LOPEZ-PELEGRIN, JRNL AUTH 5 I.GARCIA-FERRER,T.GUEVARA,V.DIVE,M.L.ZANI,T.MOREAU, JRNL AUTH 6 J.POTEMPA,F.X.GOMIS-RUTH JRNL TITL A UNIQUE NETWORK OF ATTACK, DEFENCE AND COMPETENCE ON THE JRNL TITL 2 OUTER MEMBRANE OF THE PERIODONTITIS PATHOGEN TANNERELLA JRNL TITL 3 FORSYTHIA. JRNL REF CHEM SCI V. 14 869 2023 JRNL REFN ISSN 2041-6520 JRNL PMID 36755705 JRNL DOI 10.1039/D2SC04166A REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.280 REMARK 3 FREE R VALUE TEST SET COUNT : 549 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.08 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2823 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2182 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2668 REMARK 3 BIN R VALUE (WORKING SET) : 0.2168 REMARK 3 BIN FREE R VALUE : 0.2447 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.49 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.11620 REMARK 3 B22 (A**2) : -11.61950 REMARK 3 B33 (A**2) : 7.50320 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.75450 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.230 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.134 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.113 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.128 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.111 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 899 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1219 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 418 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 21 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 126 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 899 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 111 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1074 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.95 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.94 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.71 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|27 - 127} REMARK 3 ORIGIN FOR THE GROUP (A): -15.0505 -18.5007 13.0753 REMARK 3 T TENSOR REMARK 3 T11: -0.0204 T22: -0.0004 REMARK 3 T33: 0.0332 T12: -0.0002 REMARK 3 T13: 0.0003 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.0309 L22: 0.6894 REMARK 3 L33: 2.4037 L12: -0.2453 REMARK 3 L13: 0.3077 L23: 0.0424 REMARK 3 S TENSOR REMARK 3 S11: -0.0336 S12: 0.0314 S13: 0.0087 REMARK 3 S21: -0.0623 S22: -0.0328 S23: 0.0029 REMARK 3 S31: -0.0709 S32: -0.1641 S33: 0.0664 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8EHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97925 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10402 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 41.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 8EHC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NATIVE POTE AT 9.2 MG/ML IN 50 MM REMARK 280 SODIUM CHLORIDE, 5 MM TRIS-HCL PH 8.0 WAS CRYSTALLISED FROM 20% REMARK 280 (W/V) PEG 8,000, 100 MM HEPES PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 43.46000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.46000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.28000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 332 LIES ON A SPECIAL POSITION. 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 LYS A 2 REMARK 465 GLN A 3 REMARK 465 GLN A 4 REMARK 465 ILE A 5 REMARK 465 ILE A 6 REMARK 465 LEU A 7 REMARK 465 TRP A 8 REMARK 465 ILE A 9 REMARK 465 GLY A 10 REMARK 465 VAL A 11 REMARK 465 LEU A 12 REMARK 465 LEU A 13 REMARK 465 LEU A 14 REMARK 465 LEU A 15 REMARK 465 ILE A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 VAL A 19 REMARK 465 GLY A 20 REMARK 465 CYS A 21 REMARK 465 GLU A 22 REMARK 465 ASN A 23 REMARK 465 GLY A 24 REMARK 465 GLN A 25 REMARK 465 LEU A 26 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 94 -1.12 72.29 REMARK 500 ARG A 103 -124.03 51.34 REMARK 500 ASP A 112 37.50 -97.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8EHC RELATED DB: PDB DBREF1 8EHD A 1 127 UNP A0A1D3UL35_TANFO DBREF2 8EHD A A0A1D3UL35 1 127 SEQRES 1 A 127 MET LYS GLN GLN ILE ILE LEU TRP ILE GLY VAL LEU LEU SEQRES 2 A 127 LEU LEU ILE GLY GLY VAL GLY CYS GLU ASN GLY GLN LEU SEQRES 3 A 127 HIS SER PRO PRO ALA ASN PRO GLU GLN ALA ILE LEU GLY SEQRES 4 A 127 LYS TRP GLU LEU ILE ASN SER GLY GLY ARG PRO ILE ILE SEQRES 5 A 127 PRO THR GLY TYR ARG GLU PHE LEU PRO SER GLY ILE VAL SEQRES 6 A 127 HIS LYS TYR ASP TYR THR LYS GLU GLN TYR THR SER PHE SEQRES 7 A 127 GLN CYS GLU TYR SER ILE LEU ASN ASP THR VAL LEU LEU SEQRES 8 A 127 MET CYS ASN TYR ARG TYR LYS TYR LEU PHE TYR ARG ASP SEQRES 9 A 127 LYS MET GLN LEU PHE PRO LEU ASP LEU ILE ALA ILE ARG SEQRES 10 A 127 ASP LEU THR GLU ILE TYR GLN ARG LYS LYS HET EPE A 201 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 HOH *88(H2 O) HELIX 1 AA1 ASN A 32 ILE A 37 1 6 SHEET 1 AA1 5 ARG A 49 PRO A 50 0 SHEET 2 AA1 5 GLY A 39 SER A 46 -1 N SER A 46 O ARG A 49 SHEET 3 AA1 5 GLY A 55 PHE A 59 -1 O ARG A 57 N TRP A 41 SHEET 4 AA1 5 ILE A 64 ASP A 69 -1 O HIS A 66 N GLU A 58 SHEET 5 AA1 5 GLN A 74 TYR A 75 -1 O GLN A 74 N ASP A 69 SHEET 1 AA2 9 ARG A 49 PRO A 50 0 SHEET 2 AA2 9 GLY A 39 SER A 46 -1 N SER A 46 O ARG A 49 SHEET 3 AA2 9 GLU A 121 ARG A 125 -1 O GLN A 124 N GLU A 42 SHEET 4 AA2 9 LYS A 105 PRO A 110 -1 N MET A 106 O TYR A 123 SHEET 5 AA2 9 TYR A 95 TYR A 102 -1 N LYS A 98 O PHE A 109 SHEET 6 AA2 9 VAL A 89 MET A 92 -1 N LEU A 90 O TYR A 97 SHEET 7 AA2 9 CYS A 80 ILE A 84 -1 N SER A 83 O LEU A 91 SHEET 8 AA2 9 ILE A 64 ASP A 69 -1 N VAL A 65 O CYS A 80 SHEET 9 AA2 9 GLN A 74 TYR A 75 -1 O GLN A 74 N ASP A 69 SSBOND 1 CYS A 80 CYS A 93 1555 1555 2.06 CRYST1 86.920 36.560 37.160 90.00 105.64 90.00 C 1 2 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 0.011505 0.000000 0.003221 0.00000 SCALE2 0.000000 0.027352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027945 0.00000