HEADER IMMUNE SYSTEM 05-JUL-23 8TE6 TITLE CRYSTAL STRUCTURE OF A MULTIPLE LYSINE-TO-ARGININE SUBSTITUTION MUTANT TITLE 2 OF THE HUMAN CRIG C3B-BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: V-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN Z39IG; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VSIG4, CRIG, Z39IG, UNQ317/PRO362; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RECEPTOR, COMPLEMENT, C3B-BINDING, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.G.ABRAM,B.V.GEISBRECHT REVDAT 3 13-NOV-24 8TE6 1 REMARK REVDAT 2 24-JAN-24 8TE6 1 JRNL REVDAT 1 12-JUL-23 8TE6 0 JRNL AUTH H.DUAN,T.G.ABRAM,A.R.CRUZ,S.H.M.ROOIJAKKERS,B.V.GEISBRECHT JRNL TITL NEW INSIGHTS INTO THE COMPLEMENT RECEPTOR OF THE IG JRNL TITL 2 SUPERFAMILY OBTAINED FROM STRUCTURAL AND FUNCTIONAL STUDIES JRNL TITL 3 ON TWO MUTANTS. JRNL REF IMMUNOHORIZONS V. 7 806 2023 JRNL REFN ISSN 2573-7732 JRNL PMID 38032267 JRNL DOI 10.4049/IMMUNOHORIZONS.2300064 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 25744 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 30.4870 - 3.0139 0.96 1896 160 0.1572 0.1924 REMARK 3 2 3.0139 - 2.3926 0.99 1846 155 0.1768 0.2105 REMARK 3 3 2.3926 - 2.0902 0.98 1816 152 0.1618 0.1881 REMARK 3 4 2.0902 - 1.8991 0.93 1722 145 0.1462 0.1506 REMARK 3 5 1.8991 - 1.7630 0.96 1744 147 0.1598 0.2144 REMARK 3 6 1.7630 - 1.6591 0.96 1749 147 0.1624 0.1806 REMARK 3 7 1.6591 - 1.5760 0.95 1716 144 0.1611 0.2204 REMARK 3 8 1.5760 - 1.5074 0.94 1703 143 0.1656 0.2067 REMARK 3 9 1.5074 - 1.4494 0.90 1621 137 0.1719 0.2003 REMARK 3 10 1.4494 - 1.3994 0.93 1672 140 0.1759 0.2189 REMARK 3 11 1.3994 - 1.3556 0.92 1653 139 0.1812 0.2476 REMARK 3 12 1.3556 - 1.3169 0.91 1639 137 0.1843 0.1951 REMARK 3 13 1.3169 - 1.2822 0.91 1642 138 0.1744 0.2062 REMARK 3 14 1.2822 - 1.2510 0.74 1328 113 0.1944 0.2493 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 985 REMARK 3 ANGLE : 0.792 1345 REMARK 3 CHIRALITY : 0.088 149 REMARK 3 PLANARITY : 0.006 178 REMARK 3 DIHEDRAL : 15.152 374 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 8TE6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275744. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-20 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25835 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.34900 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH 6.5) 0.2 M REMARK 280 AMMONIUM ACETATE 30% (W/V) PEG-4000, VAPOR DIFFUSION, HANGING REMARK 280 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 15.91300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.48750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.48750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.91300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.14000 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 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 -4 REMARK 465 SER A -3 REMARK 465 THR A -2 REMARK 465 GLY A -1 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 278 O HOH A 312 1565 2.19 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 ARG A 15 -4.26 71.01 REMARK 500 ARG A 41 -77.64 -134.71 REMARK 500 HIS A 71 -21.49 -146.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8TE5 RELATED DB: PDB DBREF 8TE6 A 1 118 UNP Q9Y279 VSIG4_HUMAN 20 137 SEQADV 8TE6 GLY A -4 UNP Q9Y279 EXPRESSION TAG SEQADV 8TE6 SER A -3 UNP Q9Y279 EXPRESSION TAG SEQADV 8TE6 THR A -2 UNP Q9Y279 EXPRESSION TAG SEQADV 8TE6 GLY A -1 UNP Q9Y279 EXPRESSION TAG SEQADV 8TE6 SER A 0 UNP Q9Y279 EXPRESSION TAG SEQADV 8TE6 ARG A 15 UNP Q9Y279 LYS 34 ENGINEERED MUTATION SEQADV 8TE6 ARG A 36 UNP Q9Y279 LYS 55 ENGINEERED MUTATION SEQADV 8TE6 ARG A 62 UNP Q9Y279 LYS 81 ENGINEERED MUTATION SEQADV 8TE6 ARG A 72 UNP Q9Y279 LYS 91 ENGINEERED MUTATION SEQADV 8TE6 ARG A 110 UNP Q9Y279 LYS 129 ENGINEERED MUTATION SEQRES 1 A 123 GLY SER THR GLY SER ARG PRO ILE LEU GLU VAL PRO GLU SEQRES 2 A 123 SER VAL THR GLY PRO TRP ARG GLY ASP VAL ASN LEU PRO SEQRES 3 A 123 CYS THR TYR ASP PRO LEU GLN GLY TYR THR GLN VAL LEU SEQRES 4 A 123 VAL ARG TRP LEU VAL GLN ARG GLY SER ASP PRO VAL THR SEQRES 5 A 123 ILE PHE LEU ARG ASP SER SER GLY ASP HIS ILE GLN GLN SEQRES 6 A 123 ALA ARG TYR GLN GLY ARG LEU HIS VAL SER HIS ARG VAL SEQRES 7 A 123 PRO GLY ASP VAL SER LEU GLN LEU SER THR LEU GLU MET SEQRES 8 A 123 ASP ASP ARG SER HIS TYR THR CYS GLU VAL THR TRP GLN SEQRES 9 A 123 THR PRO ASP GLY ASN GLN VAL VAL ARG ASP ARG ILE THR SEQRES 10 A 123 GLU LEU ARG VAL GLN LYS FORMUL 2 HOH *152(H2 O) HELIX 1 AA1 GLU A 85 ARG A 89 5 5 SHEET 1 AA1 6 SER A 9 PRO A 13 0 SHEET 2 AA1 6 GLN A 105 GLN A 117 1 O GLN A 117 N GLY A 12 SHEET 3 AA1 6 SER A 90 GLN A 99 -1 N TYR A 92 O THR A 112 SHEET 4 AA1 6 THR A 31 VAL A 39 -1 N ARG A 36 O GLU A 95 SHEET 5 AA1 6 VAL A 46 ASP A 52 -1 O VAL A 46 N VAL A 39 SHEET 6 AA1 6 GLY A 55 HIS A 57 -1 O HIS A 57 N LEU A 50 SHEET 1 AA2 3 VAL A 18 LEU A 20 0 SHEET 2 AA2 3 LEU A 79 LEU A 81 -1 O LEU A 79 N LEU A 20 SHEET 3 AA2 3 LEU A 67 VAL A 69 -1 N HIS A 68 O GLN A 80 SSBOND 1 CYS A 22 CYS A 94 1555 1555 2.03 CRYST1 31.826 50.280 60.975 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 0.031421 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016400 0.00000