HEADER SIGNALING PROTEIN 22-JUL-19 6KJK TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF PORA COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-TERMINAL DOMAIN OF PORA (28-171); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N-TERMINAL GSH, A REMNANT OF THE HIS-TAG. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS ATCC 33277; SOURCE 3 ORGANISM_TAXID: 431947; SOURCE 4 STRAIN: ATCC 33277; SOURCE 5 GENE: PGN_0123; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS T9SS CARGO PROTEIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.HANDA,K.SATO,M.SHOJI,K.NAKAYAMA,K.IMADA REVDAT 2 16-DEC-20 6KJK 1 JRNL REVDAT 1 22-JUL-20 6KJK 0 JRNL AUTH H.YUKITAKE,M.SHOJI,K.SATO,Y.HANDA,M.NAITO,K.IMADA,K.NAKAYAMA JRNL TITL PORA, A CONSERVED C-TERMINAL DOMAIN-CONTAINING PROTEIN, JRNL TITL 2 IMPACTS THE PORXY-SIGP SIGNALING OF THE TYPE IX SECRETION JRNL TITL 3 SYSTEM. JRNL REF SCI REP V. 10 21109 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 33273542 JRNL DOI 10.1038/S41598-020-77987-Y REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 31128 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) : 0.181 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 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 46.0700 - 2.8900 0.95 2760 139 0.1625 0.1665 REMARK 3 2 2.8900 - 2.2900 0.97 2777 144 0.1902 0.2219 REMARK 3 3 2.2900 - 2.0000 0.94 2650 141 0.1764 0.2229 REMARK 3 4 2.0000 - 1.8200 0.97 2716 163 0.1819 0.2037 REMARK 3 5 1.8200 - 1.6900 0.97 2722 154 0.1811 0.1978 REMARK 3 6 1.6900 - 1.5900 0.92 2601 125 0.1894 0.2067 REMARK 3 7 1.5900 - 1.5100 0.95 2689 145 0.1947 0.2289 REMARK 3 8 1.5100 - 1.4500 0.97 2715 157 0.2028 0.2270 REMARK 3 9 1.4500 - 1.3900 0.91 2548 125 0.2170 0.2404 REMARK 3 10 1.3900 - 1.3400 0.95 2677 152 0.2132 0.2499 REMARK 3 11 1.3400 - 1.3000 0.96 2683 145 0.2261 0.2594 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.131 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.19 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 : 0.009 1026 REMARK 3 ANGLE : 1.057 1395 REMARK 3 CHIRALITY : 0.103 161 REMARK 3 PLANARITY : 0.008 184 REMARK 3 DIHEDRAL : 3.594 592 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 6KJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31131 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M (NH4)2SO4, 26%(W/V) PEG-8000, PH REMARK 280 5.3, VAPOR DIFFUSION, SITTING 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 33.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.65000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.61000 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 253 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 301 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 GLY A 25 REMARK 465 SER A 26 REMARK 465 HIS A 27 REMARK 465 THR A 162 REMARK 465 ASP A 163 REMARK 465 LEU A 164 REMARK 465 THR A 165 REMARK 465 ASN A 166 REMARK 465 ILE A 167 REMARK 465 GLY A 168 REMARK 465 LEU A 169 REMARK 465 GLY A 170 REMARK 465 ARG A 171 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 O HOH A 217 O HOH A 277 1.86 REMARK 500 O HOH A 201 O HOH A 303 2.04 REMARK 500 O GLU A 108 O HOH A 201 2.08 REMARK 500 N ASP A 86 O HOH A 202 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 35 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES 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 GLU A 140 -38.06 -37.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KJK A 28 171 UNP B2RGZ7 B2RGZ7_PORG3 28 171 SEQADV 6KJK GLY A 25 UNP B2RGZ7 EXPRESSION TAG SEQADV 6KJK SER A 26 UNP B2RGZ7 EXPRESSION TAG SEQADV 6KJK HIS A 27 UNP B2RGZ7 EXPRESSION TAG SEQRES 1 A 147 GLY SER HIS GLN VAL VAL ILE LYS VAL GLY ASP ALA ILE SEQRES 2 A 147 LEU GLU ASN ASN ALA THR VAL ASP ILE THR ALA PHE THR SEQRES 3 A 147 THR GLU ASP GLY THR GLU GLU MET LYS PHE LYS GLY MET SEQRES 4 A 147 VAL ILE ASN GLN SER ALA THR PRO ILE ASN VAL ILE GLY SEQRES 5 A 147 LYS ILE THR LYS GLN GLU MET ILE GLY ASP GLY HIS PHE SEQRES 6 A 147 ALA LEU CYS PHE GLY GLN CYS MET LEU PRO ASN VAL SER SEQRES 7 A 147 VAL SER PRO VAL VAL GLU VAL GLY GLY GLU GLY GLU PRO SEQRES 8 A 147 LEU SER LEU ARG TYR THR PHE PRO VAL SER ASN GLU GLY SEQRES 9 A 147 HIS THR GLY ALA PHE THR PHE SER CYS PHE PRO GLU SER SEQRES 10 A 147 GLY ALA PRO GLY THR GLU LEU ALA THR VAL ASN ILE ASN SEQRES 11 A 147 PHE LYS TYR LYS GLY GLY GLY THR ASP LEU THR ASN ILE SEQRES 12 A 147 GLY LEU GLY ARG FORMUL 2 HOH *145(H2 O) HELIX 1 AA1 LYS A 158 GLY A 160 5 3 SHEET 1 AA1 4 ALA A 36 ILE A 37 0 SHEET 2 AA1 4 VAL A 29 VAL A 33 -1 N VAL A 33 O ALA A 36 SHEET 3 AA1 4 THR A 55 ASN A 66 -1 O ILE A 65 N VAL A 30 SHEET 4 AA1 4 THR A 50 GLU A 52 -1 N GLU A 52 O THR A 55 SHEET 1 AA2 5 ALA A 36 ILE A 37 0 SHEET 2 AA2 5 VAL A 29 VAL A 33 -1 N VAL A 33 O ALA A 36 SHEET 3 AA2 5 THR A 55 ASN A 66 -1 O ILE A 65 N VAL A 30 SHEET 4 AA2 5 GLU A 114 PRO A 123 -1 O PHE A 122 N GLU A 56 SHEET 5 AA2 5 HIS A 88 PHE A 93 -1 N CYS A 92 O SER A 117 SHEET 1 AA3 5 ALA A 42 ILE A 46 0 SHEET 2 AA3 5 ALA A 149 TYR A 157 1 O ASN A 154 N ILE A 46 SHEET 3 AA3 5 HIS A 129 PRO A 139 -1 N GLY A 131 O PHE A 155 SHEET 4 AA3 5 ILE A 72 GLU A 82 -1 N ILE A 75 O PHE A 138 SHEET 5 AA3 5 VAL A 107 VAL A 109 -1 O VAL A 107 N VAL A 74 SSBOND 1 CYS A 92 CYS A 96 1555 1555 2.09 CRYST1 67.300 43.220 48.590 90.00 108.52 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 0.014859 0.000000 0.004977 0.00000 SCALE2 0.000000 0.023137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021704 0.00000