HEADER IMMUNE SYSTEM 16-NOV-17 6EZW TITLE CRYSTAL STRUCTURE OF A LLAMA VHH ANTIBODY BCD090-M2 AGAINST HUMAN TITLE 2 ERBB3 IN SPACE GROUP C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VHH ANTIBODY BCD090-M2; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VHH, LLAMA ANTIBODY, SINGLE-DOMAIN ANTIBODY, NANOBODY, ERBB3, HER3, KEYWDS 2 RECEPTOR TYROSINE KINASE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR I.E.ELISEEV,A.N.YUDENKO,V.V.VYSOCHINSKAYA,A.A.SVIRINA, AUTHOR 2 A.V.EVSTRATYEVA,M.S.DROZHZHACHIH,E.A.KRENDELEVA,A.K.VLADIMIROVA, AUTHOR 3 T.A.NEMANKIN,V.M.EKIMOVA,A.B.ULITIN,M.I.LOMOVSKAYA,P.A.YAKOVLEV, AUTHOR 4 F.V.MOISEENKO,O.B.CHAKCHIR REVDAT 3 17-JAN-24 6EZW 1 JRNL REVDAT 2 28-NOV-18 6EZW 1 JRNL REVDAT 1 29-NOV-17 6EZW 0 JRNL AUTH I.E.ELISEEV,A.N.YUDENKO,V.V.VYSOCHINSKAYA,A.A.SVIRINA, JRNL AUTH 2 A.V.EVSTRATYEVA,M.S.DROZHZHACHIH,E.A.KRENDELEVA, JRNL AUTH 3 A.K.VLADIMIROVA,T.A.NEMANKIN,V.M.EKIMOVA,A.B.ULITIN, JRNL AUTH 4 M.I.LOMOVSKAYA,P.A.YAKOVLEV,A.S.BUKATIN,N.A.KNYAZEV, JRNL AUTH 5 F.V.MOISEENKO,O.B.CHAKCHIR JRNL TITL CRYSTAL STRUCTURES OF A LLAMA VHH ANTIBODY BCD090-M2 JRNL TITL 2 TARGETING HUMAN ERBB3 RECEPTOR. JRNL REF F1000RES V. 7 57 2018 JRNL REFN ESSN 2046-1402 JRNL PMID 30430004 JRNL DOI 10.12688/F1000RESEARCH.13612.1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 15157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.009 REMARK 3 FREE R VALUE TEST SET COUNT : 1517 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 33.3047 - 3.5536 0.99 1327 149 0.1635 0.1934 REMARK 3 2 3.5536 - 2.8210 1.00 1300 143 0.1644 0.2109 REMARK 3 3 2.8210 - 2.4646 0.99 1276 142 0.1896 0.2092 REMARK 3 4 2.4646 - 2.2393 0.99 1268 141 0.1820 0.2275 REMARK 3 5 2.2393 - 2.0788 0.99 1271 143 0.1796 0.1877 REMARK 3 6 2.0788 - 1.9563 0.98 1255 139 0.1717 0.1948 REMARK 3 7 1.9563 - 1.8583 0.98 1248 136 0.1816 0.2413 REMARK 3 8 1.8583 - 1.7774 0.97 1237 136 0.1891 0.2007 REMARK 3 9 1.7774 - 1.7090 0.95 1213 136 0.1996 0.2238 REMARK 3 10 1.7090 - 1.6500 0.96 1216 138 0.2396 0.2653 REMARK 3 11 1.6500 - 1.5984 0.80 1029 114 0.2781 0.2825 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) : 0.142 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.702 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.36 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 : 0.006 1003 REMARK 3 ANGLE : 0.823 1357 REMARK 3 CHIRALITY : 0.056 140 REMARK 3 PLANARITY : 0.005 179 REMARK 3 DIHEDRAL : 16.318 361 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 6EZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER IMUS MICROFOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT V8.18C REMARK 200 DATA SCALING SOFTWARE : SADABS 2008/1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.598 REMARK 200 RESOLUTION RANGE LOW (A) : 33.298 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.214 REMARK 200 R MERGE (I) : 0.07317 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7359 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38663 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.070 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: 5IMK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 0.1M MES-IMIDAZOLE REMARK 280 PH 6.5, 0.02M SODIUM FORMATE, 0.02M AMMONIUM ACETATE, 0.02M REMARK 280 SODIUM CITRATE, 0.02M SODIUM POTASSIUM TARTRATE, 0.02M SODIUM REMARK 280 OXAMATE, 20% V/V PEG 500MME, 10% W/V PEG 20 000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K 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 32.87950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.46550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.87950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.46550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 214 O HOH B 257 1.97 REMARK 500 O GLY B 1 O HOH B 201 1.98 REMARK 500 O GLY B 27 O HOH B 202 2.02 REMARK 500 O HOH B 303 O HOH B 376 2.05 REMARK 500 O HOH B 241 O HOH B 326 2.06 REMARK 500 O HOH B 277 O HOH B 389 2.08 REMARK 500 O HOH B 320 O HOH B 388 2.09 REMARK 500 O HOH B 214 O HOH B 217 2.10 REMARK 500 N GLY B 1 O HOH B 203 2.12 REMARK 500 OE1 GLN B 109 O HOH B 204 2.14 REMARK 500 O HOH B 288 O HOH B 369 2.15 REMARK 500 O HOH B 299 O HOH B 360 2.15 REMARK 500 O HOH B 245 O HOH B 339 2.18 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 B 371 O HOH B 385 3545 2.00 REMARK 500 O HOH B 212 O HOH B 360 4456 2.06 REMARK 500 O HOH B 323 O HOH B 359 4446 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 THR B 29 73.46 60.15 REMARK 500 ALA B 93 167.02 179.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 6EZW B 1 128 PDB 6EZW 6EZW 1 128 SEQRES 1 B 128 GLY GLN VAL GLN LEU VAL GLN SER GLY GLY GLY LEU VAL SEQRES 2 B 128 GLN ALA GLY GLY SER LEU ARG LEU SER CYS ALA PHE SER SEQRES 3 B 128 GLY ARG THR PHE SER MET TYR THR MET GLY TRP PHE ARG SEQRES 4 B 128 GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ASN SEQRES 5 B 128 ARG GLY ARG GLY LEU SER PRO ASP ILE ALA ASP SER VAL SEQRES 6 B 128 ASN GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 128 THR LEU TYR LEU GLN MET ASP SER LEU LYS PRO GLU ASP SEQRES 8 B 128 THR ALA VAL TYR TYR CYS ALA ALA ASP LEU GLN TYR GLY SEQRES 9 B 128 SER SER TRP PRO GLN ARG SER SER ALA GLU TYR ASP TYR SEQRES 10 B 128 TRP GLY GLN GLY THR THR VAL THR VAL SER SER FORMUL 2 HOH *190(H2 O) HELIX 1 AA1 THR B 29 SER B 31 5 3 HELIX 2 AA2 LYS B 88 THR B 92 5 5 HELIX 3 AA3 SER B 111 TYR B 115 5 5 SHEET 1 AA1 4 GLN B 4 SER B 8 0 SHEET 2 AA1 4 LEU B 19 SER B 26 -1 O ALA B 24 N VAL B 6 SHEET 3 AA1 4 THR B 79 MET B 84 -1 O MET B 84 N LEU B 19 SHEET 4 AA1 4 PHE B 69 ASP B 74 -1 N SER B 72 O TYR B 81 SHEET 1 AA2 6 GLY B 11 GLN B 14 0 SHEET 2 AA2 6 THR B 122 SER B 127 1 O SER B 127 N VAL B 13 SHEET 3 AA2 6 ALA B 93 LEU B 101 -1 N TYR B 95 O THR B 122 SHEET 4 AA2 6 TYR B 33 GLN B 40 -1 N PHE B 38 O TYR B 96 SHEET 5 AA2 6 GLU B 47 ASN B 52 -1 O ALA B 50 N TRP B 37 SHEET 6 AA2 6 ASP B 60 ILE B 61 -1 O ASP B 60 N ALA B 51 SHEET 1 AA3 4 GLY B 11 GLN B 14 0 SHEET 2 AA3 4 THR B 122 SER B 127 1 O SER B 127 N VAL B 13 SHEET 3 AA3 4 ALA B 93 LEU B 101 -1 N TYR B 95 O THR B 122 SHEET 4 AA3 4 TYR B 117 TRP B 118 -1 O TYR B 117 N ALA B 99 SSBOND 1 CYS B 23 CYS B 97 1555 1555 2.05 CISPEP 1 TRP B 107 PRO B 108 0 -5.70 CRYST1 65.759 38.931 47.482 90.00 102.24 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 0.015207 0.000000 0.003300 0.00000 SCALE2 0.000000 0.025686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021551 0.00000