HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 01-NOV-06 2NR7 TITLE STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF PUTATIVE SECRETION TITLE 2 ACTIVATOR PROTEIN FROM PORPHYROMONAS GINGIVALIS W83 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETION ACTIVATOR PROTEIN, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 242619; SOURCE 4 STRAIN: W83; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCGS19 KEYWDS APCC85792, SECRETION ACTIVATOR, PORPHYROMONAS GINGIVALIS W83, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MCSG, KEYWDS 3 MIDWEST CENTER FOR STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,L.BIGELOW,M.GU,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 4 27-DEC-23 2NR7 1 SEQADV LINK REVDAT 3 13-JUL-11 2NR7 1 VERSN REVDAT 2 24-FEB-09 2NR7 1 VERSN REVDAT 1 05-DEC-06 2NR7 0 JRNL AUTH K.TAN,L.BIGELOW,M.GU,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF PUTATIVE SECRETION ACTIVATOR JRNL TITL 2 PROTEIN FROM PORPHYROMONAS GINGIVALIS W83 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 40037 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2145 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2255 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.060 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1595 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2157 ; 1.324 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 5.487 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;32.549 ;23.924 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 287 ;11.178 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.984 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 235 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1206 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 864 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1100 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 330 ; 0.137 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 71 ; 0.185 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 83 ; 0.152 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 979 ; 1.023 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1538 ; 1.571 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 710 ; 3.108 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 619 ; 3.251 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1689 ; 3.075 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 441 ; 3.304 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1564 ; 2.818 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2NR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42196 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0000 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) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS TRIS PH5.5, 25% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 47.26850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.19300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.26850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.19300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE REMARK 300 FOR THE PROTEIN IS UNKNOWN. 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 SER A -2 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 VAL A 41 78.65 -115.32 REMARK 500 VAL A 68 -69.31 -126.07 REMARK 500 TYR A 73 -60.02 -124.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC85792 RELATED DB: TARGETDB DBREF 2NR7 A 1 192 UNP Q7MXB3 Q7MXB3_PORGI 1 192 SEQADV 2NR7 SER A -2 UNP Q7MXB3 CLONING ARTIFACT SEQADV 2NR7 ASN A -1 UNP Q7MXB3 CLONING ARTIFACT SEQADV 2NR7 ALA A 0 UNP Q7MXB3 CLONING ARTIFACT SEQADV 2NR7 MSE A 1 UNP Q7MXB3 MET 1 MODIFIED RESIDUE SEQRES 1 A 195 SER ASN ALA MSE ALA ASN VAL LYS LEU LEU LEU PRO TYR SEQRES 2 A 195 ILE LEU LYS TRP GLU GLY GLY PHE VAL HIS ASP PRO ALA SEQRES 3 A 195 ASP ALA GLY GLY ALA THR ASN LYS GLY VAL THR ILE ALA SEQRES 4 A 195 THR TRP LYS ARG VAL GLY TYR ASP LYS ASP GLY ASP GLY SEQRES 5 A 195 ASP ILE ASP VAL GLU ASP LEU LYS LEU LEU THR ASP ASP SEQRES 6 A 195 ASP VAL LEU ASN ARG VAL LEU LYS PRO PHE TYR TRP ASP SEQRES 7 A 195 ARG TRP LYS ALA ASP LEU ILE GLU SER GLN LYS VAL ALA SEQRES 8 A 195 ASN ILE LEU VAL ASP TRP VAL TRP GLY SER GLY LYS TYR SEQRES 9 A 195 GLY ILE VAL ILE PRO GLN ARG ILE LEU GLY VAL GLN ALA SEQRES 10 A 195 ASP GLY ILE VAL GLY ASN LYS THR LEU GLN ALA VAL ASN SEQRES 11 A 195 SER ALA ASP PRO ASP GLU LEU PHE GLU SER ILE PHE ASP SEQRES 12 A 195 ALA ARG ARG GLU PHE LEU GLU ASP ILE THR ALA ARG SER SEQRES 13 A 195 ILE LYS LYS TYR GLU ASP SER ILE GLY ARG LYS ALA THR SEQRES 14 A 195 GLU ARG GLU LEU LEU ARG HIS THR ASN LYS ARG PHE LEU SEQRES 15 A 195 ARG GLY TRP LEU ASN ARG LEU GLU ASP ILE ARG LYS LEU MODRES 2NR7 MSE A 1 MET SELENOMETHIONINE HET MSE A 1 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *410(H2 O) HELIX 1 1 ASN A 3 GLY A 17 1 15 HELIX 2 2 PRO A 22 GLY A 26 5 5 HELIX 3 3 ASP A 55 LEU A 59 5 5 HELIX 4 4 THR A 60 VAL A 68 1 9 HELIX 5 5 VAL A 68 TYR A 73 1 6 HELIX 6 6 TRP A 74 ILE A 82 5 9 HELIX 7 7 SER A 84 GLY A 99 1 16 HELIX 8 8 LYS A 100 GLY A 111 1 12 HELIX 9 9 GLY A 119 ALA A 129 1 11 HELIX 10 10 ASP A 130 GLY A 162 1 33 HELIX 11 11 THR A 166 THR A 174 1 9 HELIX 12 12 ASN A 175 ILE A 189 1 15 HELIX 13 13 ARG A 190 LEU A 192 5 3 SHEET 1 A 2 PHE A 18 HIS A 20 0 SHEET 2 A 2 THR A 29 LYS A 31 -1 O ASN A 30 N VAL A 19 LINK C ALA A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 CRYST1 94.537 36.386 62.474 90.00 119.75 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 0.010578 0.000000 0.006046 0.00000 SCALE2 0.000000 0.027483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018437 0.00000