HEADER IMMUNE SYSTEM 08-MAR-18 6CNE TITLE SELENOMETHIONINE VARIANT (V29SEM) OF PROTEIN GB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IGG-BINDING PROTEIN G; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP. GROUP G; SOURCE 3 ORGANISM_TAXID: 1320; SOURCE 4 GENE: SPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: BL21DE3 KEYWDS IMMUNOGLOBULIN G-BINDING PROTEIN DOMAIN B1, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Q.CHEN REVDAT 6 15-NOV-23 6CNE 1 REMARK REVDAT 5 04-OCT-23 6CNE 1 REMARK REVDAT 4 12-FEB-20 6CNE 1 JRNL REVDAT 3 22-JAN-20 6CNE 1 TITLE JRNL REVDAT 2 27-NOV-19 6CNE 1 REMARK REVDAT 1 10-JUL-19 6CNE 0 JRNL AUTH Q.CHEN,S.XU,X.LU,M.V.BOERI,Y.PEPELYAYEVA,E.L.DIAZ,S.D.SONI, JRNL AUTH 2 M.ALLAIRE,M.B.FORSTNER,B.J.BAHNSON,S.ROZOVSKY JRNL TITL 77SE NMR PROBES THE PROTEIN ENVIRONMENT OF SELENOMETHIONINE. JRNL REF J.PHYS.CHEM.B V. 124 601 2020 JRNL REFN ISSN 1089-5647 JRNL PMID 31846581 JRNL DOI 10.1021/ACS.JPCB.9B07466 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 56936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1916 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 27.4873 - 2.8911 0.99 4065 143 0.1853 0.1895 REMARK 3 2 2.8911 - 2.2951 0.99 4064 144 0.1888 0.2101 REMARK 3 3 2.2951 - 2.0051 0.98 4040 137 0.1631 0.1815 REMARK 3 4 2.0051 - 1.8218 0.99 4057 139 0.1532 0.1927 REMARK 3 5 1.8218 - 1.6913 0.98 4003 139 0.1529 0.2150 REMARK 3 6 1.6913 - 1.5916 0.98 4009 141 0.1434 0.1767 REMARK 3 7 1.5916 - 1.5119 0.97 4031 142 0.1388 0.1890 REMARK 3 8 1.5119 - 1.4461 0.97 3938 137 0.1436 0.1858 REMARK 3 9 1.4461 - 1.3904 0.93 3798 129 0.1603 0.2096 REMARK 3 10 1.3904 - 1.3424 0.95 3932 142 0.1621 0.1728 REMARK 3 11 1.3424 - 1.3004 0.94 3809 130 0.1705 0.2507 REMARK 3 12 1.3004 - 1.2633 0.94 3891 136 0.1705 0.2154 REMARK 3 13 1.2633 - 1.2300 0.94 3821 136 0.1773 0.2146 REMARK 3 14 1.2300 - 1.2000 0.87 3562 121 0.2085 0.2354 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 928 REMARK 3 ANGLE : 1.195 1264 REMARK 3 CHIRALITY : 0.089 143 REMARK 3 PLANARITY : 0.007 157 REMARK 3 DIHEDRAL : 19.851 326 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 6CNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6-4.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : ASYMMETRICC CURVED CRYST REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05208 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47140 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2QMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 47% MPD 20% IPA 25 MM SODIUM ACETATE REMARK 280 PH 4.9 20 MG/ML PROTEIN IN 25 MM SODIUM ACETATE BUFFER PH 5.5 REMARK 280 NON-REDUCING CONDITIONS (NO TCEP), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 283.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 18.21500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 B 202 O HOH B 213 1.87 REMARK 500 OD2 ASP B 36 O HOH B 201 1.90 REMARK 500 OD2 ASP B 40 O HOH B 202 1.90 REMARK 500 O4 MPD A 102 O HOH A 201 1.93 REMARK 500 OE1 GLU A 42 O HOH A 202 1.94 REMARK 500 OE2 GLU B 42 O HOH B 203 2.04 REMARK 500 NZ LYS A 50 O HOH A 203 2.09 REMARK 500 O HOH A 203 O HOH A 245 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 219 O HOH B 247 1554 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 103 DBREF 6CNE A 3 56 UNP P06654 SPG1_STRSG 229 282 DBREF 6CNE B 3 56 UNP P06654 SPG1_STRSG 229 282 SEQADV 6CNE GLY A 1 UNP P06654 EXPRESSION TAG SEQADV 6CNE GLN A 2 UNP P06654 EXPRESSION TAG SEQADV 6CNE MSE A 5 UNP P06654 LEU 231 ENGINEERED MUTATION SEQADV 6CNE GLY B 1 UNP P06654 EXPRESSION TAG SEQADV 6CNE GLN B 2 UNP P06654 EXPRESSION TAG SEQADV 6CNE MSE B 5 UNP P06654 LEU 231 ENGINEERED MUTATION SEQRES 1 A 56 GLY GLN TYR LYS MSE ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 A 56 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 A 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 56 THR VAL THR GLU SEQRES 1 B 56 GLY GLN TYR LYS MSE ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 B 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 B 56 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 B 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 B 56 THR VAL THR GLU HET MSE A 5 17 HET MSE B 5 17 HET MPD A 101 22 HET MPD A 102 22 HET PO4 A 103 5 HET MPD B 101 22 HET MPD B 102 22 HET PO4 B 103 5 HETNAM MSE SELENOMETHIONINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 MPD 4(C6 H14 O2) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *176(H2 O) HELIX 1 AA1 ASP A 22 ASN A 37 1 16 HELIX 2 AA2 ASP B 22 ASN B 37 1 16 SHEET 1 AA1 4 LYS A 13 GLU A 19 0 SHEET 2 AA1 4 GLN A 2 ASN A 8 -1 N TYR A 3 O THR A 18 SHEET 3 AA1 4 THR A 51 THR A 55 1 O PHE A 52 N LYS A 4 SHEET 4 AA1 4 GLU A 42 ASP A 46 -1 N GLU A 42 O THR A 55 SHEET 1 AA2 4 LYS B 13 GLU B 19 0 SHEET 2 AA2 4 GLN B 2 ASN B 8 -1 N TYR B 3 O THR B 18 SHEET 3 AA2 4 THR B 51 THR B 55 1 O PHE B 52 N LYS B 4 SHEET 4 AA2 4 GLU B 42 ASP B 46 -1 N GLU B 42 O THR B 55 LINK C LYS A 4 N MSE A 5 1555 1555 1.34 LINK C MSE A 5 N ILE A 6 1555 1555 1.33 LINK C LYS B 4 N MSE B 5 1555 1555 1.34 LINK C MSE B 5 N ILE B 6 1555 1555 1.32 SITE 1 AC1 6 ASN A 8 THR A 44 THR A 53 THR A 55 SITE 2 AC1 6 HOH A 213 HOH A 226 SITE 1 AC2 4 LYS A 13 GLY A 14 HOH A 201 HOH A 204 SITE 1 AC3 4 ALA A 23 GLU A 27 TYR A 45 HOH A 246 SITE 1 AC4 5 ASN B 8 THR B 53 THR B 55 HOH B 211 SITE 2 AC4 5 HOH B 224 SITE 1 AC5 5 LYS B 10 THR B 11 LYS B 13 GLN B 32 SITE 2 AC5 5 HOH B 255 SITE 1 AC6 3 LYS B 13 GLY B 14 HOH B 222 CRYST1 27.844 36.430 48.963 90.00 99.27 90.00 P 1 21 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 0.035914 0.000000 0.005862 0.00000 SCALE2 0.000000 0.027450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020694 0.00000