HEADER IMMUNE SYSTEM 10-APR-13 4K3G TITLE IMMUNOGLOBULIN LAMBDA VARIABLE DOMAIN L5(L89S) FLUOROGEN ACTIVATING TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN LAMBDA VARIABLE DOMAIN L5(L89S); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: YVH10 KEYWDS IMMUNOGLOBULIN FOLD, FLUORESCENCE, MALACHITE GREEN, O-MANNOSYLATION, KEYWDS 2 THR27, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.L.STANFIELD,C.SZENT-GYORGYI,I.A.WILSON REVDAT 3 29-JUL-20 4K3G 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 13-NOV-13 4K3G 1 JRNL REVDAT 1 09-OCT-13 4K3G 0 JRNL AUTH C.SZENT-GYORGYI,R.L.STANFIELD,S.ANDREKO,A.DEMPSEY,M.AHMED, JRNL AUTH 2 S.CAPEK,A.S.WAGGONER,I.A.WILSON,M.P.BRUCHEZ JRNL TITL MALACHITE GREEN MEDIATES HOMODIMERIZATION OF ANTIBODY VL JRNL TITL 2 DOMAINS TO FORM A FLUORESCENT TERNARY COMPLEX WITH SINGULAR JRNL TITL 3 SYMMETRIC INTERFACES. JRNL REF J.MOL.BIOL. V. 425 4595 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23978698 JRNL DOI 10.1016/J.JMB.2013.08.014 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21259 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1094 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 27.4343 - 3.8527 1.00 2555 136 0.1577 0.1868 REMARK 3 2 3.8527 - 3.0593 1.00 2527 131 0.1798 0.2099 REMARK 3 3 3.0593 - 2.6730 1.00 2505 153 0.1992 0.2571 REMARK 3 4 2.6730 - 2.4288 1.00 2525 141 0.2070 0.2424 REMARK 3 5 2.4288 - 2.2548 1.00 2530 121 0.2098 0.2849 REMARK 3 6 2.2548 - 2.1219 1.00 2502 142 0.2186 0.2340 REMARK 3 7 2.1219 - 2.0156 1.00 2499 129 0.2411 0.2849 REMARK 3 8 2.0156 - 1.9279 0.99 2522 141 0.2885 0.3355 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 : 0.40 REMARK 3 B_SOL : 61.63 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.77980 REMARK 3 B22 (A**2) : 2.77980 REMARK 3 B33 (A**2) : -5.55960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 1712 REMARK 3 ANGLE : 1.193 2343 REMARK 3 CHIRALITY : 0.080 267 REMARK 3 PLANARITY : 0.006 302 REMARK 3 DIHEDRAL : 12.892 611 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 4K3G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 27.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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 (%): 57.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 10% 2-METHYL-2,3 REMARK 280 -PENTANEDIOL , PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 47.66000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.83000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.49000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLN A 1 REMARK 465 THR A 108 REMARK 465 GLY A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 SER B 107 REMARK 465 THR B 108 REMARK 465 GLY B 109 REMARK 465 HIS B 110 REMARK 465 HIS B 111 REMARK 465 HIS B 112 REMARK 465 HIS B 113 REMARK 465 HIS B 114 REMARK 465 HIS B 115 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 THR A 51 -49.67 72.65 REMARK 500 ALA A 84 168.53 172.84 REMARK 500 THR B 51 -47.71 73.85 REMARK 500 ALA B 78 141.28 -38.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K3H RELATED DB: PDB DBREF 4K3G A 1 115 PDB 4K3G 4K3G 1 115 DBREF 4K3G B 1 115 PDB 4K3G 4K3G 1 115 SEQRES 1 A 118 GLN ALA VAL VAL THR GLN GLU PRO SER VAL THR VAL SER SEQRES 2 A 118 PRO GLY GLY THR VAL ILE LEU THR CYS GLY SER SER THR SEQRES 3 A 118 GLY ALA VAL THR SER GLY HIS TYR ALA ASN TRP PHE GLN SEQRES 4 A 118 GLN LYS PRO GLY GLN ALA PRO ARG ALA LEU ILE PHE GLU SEQRES 5 A 118 THR ASP LYS LYS TYR SER TRP THR PRO GLY ARG PHE SER SEQRES 6 A 118 GLY SER LEU LEU GLY ALA LYS ALA ALA LEU THR ILE SER SEQRES 7 A 118 ASP ALA GLN PRO GLU ASP GLU ALA GLU TYR TYR CYS SER SEQRES 8 A 118 LEU SER ASP VAL ASP GLY TYR LEU PHE GLY GLY GLY THR SEQRES 9 A 118 GLN LEU THR VAL LEU SER THR GLY HIS HIS HIS HIS HIS SEQRES 10 A 118 HIS SEQRES 1 B 118 GLN ALA VAL VAL THR GLN GLU PRO SER VAL THR VAL SER SEQRES 2 B 118 PRO GLY GLY THR VAL ILE LEU THR CYS GLY SER SER THR SEQRES 3 B 118 GLY ALA VAL THR SER GLY HIS TYR ALA ASN TRP PHE GLN SEQRES 4 B 118 GLN LYS PRO GLY GLN ALA PRO ARG ALA LEU ILE PHE GLU SEQRES 5 B 118 THR ASP LYS LYS TYR SER TRP THR PRO GLY ARG PHE SER SEQRES 6 B 118 GLY SER LEU LEU GLY ALA LYS ALA ALA LEU THR ILE SER SEQRES 7 B 118 ASP ALA GLN PRO GLU ASP GLU ALA GLU TYR TYR CYS SER SEQRES 8 B 118 LEU SER ASP VAL ASP GLY TYR LEU PHE GLY GLY GLY THR SEQRES 9 B 118 GLN LEU THR VAL LEU SER THR GLY HIS HIS HIS HIS HIS SEQRES 10 B 118 HIS MODRES 4K3G THR B 27 THR GLYCOSYLATION SITE HET MAN B 201 11 HETNAM MAN ALPHA-D-MANNOPYRANOSE FORMUL 3 MAN C6 H12 O6 FORMUL 4 HOH *141(H2 O) HELIX 1 1 THR A 28 TYR A 32 5 5 HELIX 2 2 GLN A 79 GLU A 83 5 5 HELIX 3 3 GLN B 79 GLU B 83 5 5 SHEET 1 A 4 VAL A 4 GLN A 6 0 SHEET 2 A 4 VAL A 19 SER A 25 -1 O GLY A 24 N THR A 5 SHEET 3 A 4 LYS A 70 ILE A 75 -1 O ALA A 71 N CYS A 23 SHEET 4 A 4 PHE A 62 LEU A 67 -1 N LEU A 67 O LYS A 70 SHEET 1 B 6 SER A 9 VAL A 13 0 SHEET 2 B 6 THR A 102 VAL A 106 1 O THR A 105 N VAL A 13 SHEET 3 B 6 ALA A 84 ASP A 92 -1 N ALA A 84 O LEU A 104 SHEET 4 B 6 ASN A 34 GLN A 38 -1 N GLN A 38 O GLU A 85 SHEET 5 B 6 ARG A 45 PHE A 49 -1 O LEU A 47 N TRP A 35 SHEET 6 B 6 LYS A 53 LYS A 54 -1 O LYS A 53 N PHE A 49 SHEET 1 C 4 SER A 9 VAL A 13 0 SHEET 2 C 4 THR A 102 VAL A 106 1 O THR A 105 N VAL A 13 SHEET 3 C 4 ALA A 84 ASP A 92 -1 N ALA A 84 O LEU A 104 SHEET 4 C 4 GLY A 95 PHE A 98 -1 O LEU A 97 N LEU A 90 SHEET 1 D 4 VAL B 4 GLN B 6 0 SHEET 2 D 4 VAL B 19 SER B 25 -1 O GLY B 24 N THR B 5 SHEET 3 D 4 LYS B 70 ILE B 75 -1 O ILE B 75 N VAL B 19 SHEET 4 D 4 PHE B 62 LEU B 67 -1 N LEU B 67 O LYS B 70 SHEET 1 E 6 SER B 9 VAL B 13 0 SHEET 2 E 6 THR B 102 VAL B 106 1 O GLN B 103 N VAL B 11 SHEET 3 E 6 ALA B 84 ASP B 92 -1 N ALA B 84 O LEU B 104 SHEET 4 E 6 TYR B 32 GLN B 38 -1 N GLN B 38 O GLU B 85 SHEET 5 E 6 ARG B 45 PHE B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 E 6 LYS B 53 LYS B 54 -1 O LYS B 53 N PHE B 49 SHEET 1 F 4 SER B 9 VAL B 13 0 SHEET 2 F 4 THR B 102 VAL B 106 1 O GLN B 103 N VAL B 11 SHEET 3 F 4 ALA B 84 ASP B 92 -1 N ALA B 84 O LEU B 104 SHEET 4 F 4 GLY B 95 PHE B 98 -1 O LEU B 97 N LEU B 90 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.03 SSBOND 2 CYS B 23 CYS B 88 1555 1555 2.03 LINK OG1 THR B 27 C1 MAN B 201 1555 1555 1.45 CRYST1 54.860 54.860 95.320 90.00 90.00 90.00 P 41 8 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 0.018227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018227 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010491 0.00000