HEADER ANTIVIRAL PROTEIN 23-DEC-22 8C3E TITLE ENGINEERED MINI-PROTEIN LCB2 (BLOCKING LIGAND OF SARS-COV-2 SPIKE TITLE 2 PROTEIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED PROTEIN LCB2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS SARS-COV-2, MINI-PROTEIN, ANTIVIRAL, BLOCKING LIGAND, ANTIVIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.A.KORBAN,O.V.MIKHAILOVSKII,D.A.LUZIK,V.V.GURZHIY,A.D.LEVKINA, AUTHOR 2 B.B.KHARKOV,N.R.SKRYNNIKOV REVDAT 3 23-JUL-25 8C3E 1 JRNL REVDAT 2 22-JAN-25 8C3E 1 COMPND REMARK ATOM REVDAT 1 12-APR-23 8C3E 0 JRNL AUTH S.A.KORBAN,O.MIKHAILOVSKII,V.V.GURZHIY,I.S.PODKORYTOV, JRNL AUTH 2 N.R.SKRYNNIKOV JRNL TITL USING MULTIPLE COMPUTER-PREDICTED STRUCTURES AS MOLECULAR JRNL TITL 2 REPLACEMENT MODELS: APPLICATION TO THE ANTIVIRAL JRNL TITL 3 MINI-PROTEIN LCB2. JRNL REF IUCRJ V. 12 488 2025 JRNL REFN ESSN 2052-2525 JRNL PMID 40549150 JRNL DOI 10.1107/S2052252525005123 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 17.790 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 4869 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 521 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 50.0700 - 3.3400 0.89 1138 134 0.2203 0.2353 REMARK 3 2 3.3400 - 2.6500 0.90 1093 118 0.2169 0.2504 REMARK 3 3 2.6500 - 2.3200 0.89 1050 135 0.2114 0.2686 REMARK 3 4 2.3200 - 2.1000 0.89 1067 134 0.2102 0.2888 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.651 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.98 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 : 0.002 493 REMARK 3 ANGLE : 0.364 650 REMARK 3 CHIRALITY : 0.027 66 REMARK 3 PLANARITY : 0.003 84 REMARK 3 DIHEDRAL : 4.755 72 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 8C3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292127250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 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 : RIGAKU PHOTONJET-S 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH4.8, 50MM REMARK 280 AMMONIUM SULFATE, 5% PEG4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.84667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.69333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.69333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.84667 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: 340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 SER A 2 REMARK 465 SER A 3 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 ASP A 5 -6.20 69.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 8C3E A 1 58 PDB 8C3E 8C3E 1 58 SEQRES 1 A 58 GLY SER SER ASP ASP GLU ASP SER VAL ARG TYR LEU LEU SEQRES 2 A 58 TYR MET ALA GLU LEU ARG TYR GLU GLN GLY ASN PRO GLU SEQRES 3 A 58 LYS ALA LYS LYS ILE LEU GLU MET ALA GLU PHE ILE ALA SEQRES 4 A 58 LYS ARG ASN ASN ASN GLU GLU LEU GLU ARG LEU VAL ARG SEQRES 5 A 58 GLU VAL LYS LYS ARG LEU HET GOL A 101 6 HET GOL A 102 6 HET GOL A 103 6 HET GOL A 104 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 HOH *18(H2 O) HELIX 1 AA1 ASP A 5 GLN A 22 1 18 HELIX 2 AA2 ASN A 24 ARG A 41 1 18 HELIX 3 AA3 ASN A 44 LEU A 58 1 15 CRYST1 57.817 57.817 41.540 90.00 90.00 120.00 P 31 2 1 6 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 0.017296 0.009986 0.000000 0.00000 SCALE2 0.000000 0.019972 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024073 0.00000 CONECT 471 472 473 CONECT 472 471 CONECT 473 471 474 475 CONECT 474 473 CONECT 475 473 476 CONECT 476 475 CONECT 477 478 479 CONECT 478 477 CONECT 479 477 480 481 CONECT 480 479 CONECT 481 479 482 CONECT 482 481 CONECT 483 484 485 CONECT 484 483 CONECT 485 483 486 487 CONECT 486 485 CONECT 487 485 488 CONECT 488 487 CONECT 489 490 491 CONECT 490 489 CONECT 491 489 492 493 CONECT 492 491 CONECT 493 491 494 CONECT 494 493 MASTER 240 0 4 3 0 0 0 6 511 1 24 5 END