HEADER DE NOVO PROTEIN 19-SEP-22 8EK4 TITLE DE NOVO DESIGNED ICE-BINDING PROTEINS FROM TWIST-CONSTRAINED HELICES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ICE-BINDING PROTEIN TIP-99A; COMPND 3 CHAIN: A, B; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO DESIGNED, ICE-BINDING PROTEINS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,R.J.DE HAAS REVDAT 2 03-APR-24 8EK4 1 REMARK REVDAT 1 12-JUL-23 8EK4 0 JRNL AUTH R.J.DE HAAS,R.P.TAS,D.VAN DEN BROEK,C.ZHENG,H.NGUYEN,A.KANG, JRNL AUTH 2 A.K.BERA,N.P.KING,I.K.VOETS,R.DE VRIES JRNL TITL DE NOVO DESIGNED ICE-BINDING PROTEINS FROM TWIST-CONSTRAINED JRNL TITL 2 HELICES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 80120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37364125 JRNL DOI 10.1073/PNAS.2220380120 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 553 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 49.9400 - 3.7300 0.99 2928 142 0.2330 0.2660 REMARK 3 2 3.7300 - 2.9600 1.00 2819 147 0.3012 0.3891 REMARK 3 3 2.9600 - 2.5900 1.00 2778 144 0.2878 0.3764 REMARK 3 4 2.5900 - 2.3500 1.00 2810 120 0.2738 0.3459 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.945 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.35 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 2171 REMARK 3 ANGLE : 0.366 2882 REMARK 3 CHIRALITY : 0.028 351 REMARK 3 PLANARITY : 0.002 352 REMARK 3 DIHEDRAL : 12.496 910 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 8EK4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-22 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11928 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 59.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.550 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: DESIGNED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02M 1,6-HEXANEDIOL, 0.02M 1-BUTANOL, REMARK 280 0.02M 1,2-PROPANEDIOL, 0.02M 2-PROPANOL, 0.02M 2-PROPANOL, 0.02M REMARK 280 1,4-BUTANEDIOL, 0.02M 1,3-PROPANEDIOL, 0.0466M PH 8.5 TRIS (BASE) REMARK 280 , 0.0534M PH 8.5 BICINE, 20% V/V PEG 500 MME, AND 10% W/V PEG 20, REMARK 280 000, VAPOR DIFFUSION, SITTING 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 27.29100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.16300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.71350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.16300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.29100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.71350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLU A 3 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 GLY A 140 REMARK 465 TRP A 141 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 SER B 138 REMARK 465 GLY B 139 REMARK 465 GLY B 140 REMARK 465 TRP B 141 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 ARG A 11 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 ARG B 6 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 ARG B 56 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 93 CG CD CE NZ REMARK 470 LYS B 98 CG CD CE NZ 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 ASN A 45 85.85 57.39 REMARK 500 LYS A 93 102.07 -58.58 REMARK 500 ASP B 92 -81.59 -143.88 REMARK 500 LEU B 97 41.34 -108.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 8EK4 A 1 141 PDB 8EK4 8EK4 1 141 DBREF 8EK4 B 1 141 PDB 8EK4 8EK4 1 141 SEQRES 1 A 141 MET GLU GLU GLU VAL ARG GLU LYS LEU LYS ARG MET GLU SEQRES 2 A 141 LYS LYS PHE ASP ASP SER LEU GLU LYS ALA GLU ARG LYS SEQRES 3 A 141 ILE ARG GLU ILE ILE LYS GLU ALA GLU LYS LYS LEU LYS SEQRES 4 A 141 THR LEU LYS LYS ARG ASN GLY PRO TYR GLU ALA VAL VAL SEQRES 5 A 141 THR THR LEU ARG ALA ILE LEU LYS ALA VAL GLU THR LYS SEQRES 6 A 141 ILE ARG ALA ILE ILE LYS ALA LEU LYS THR GLU LEU ASP SEQRES 7 A 141 ALA LEU ILE LYS ALA MET GLU THR ILE LEU LYS ALA HIS SEQRES 8 A 141 ASP LYS ASN ASP GLU LEU LYS LYS GLU VAL GLU ASP ILE SEQRES 9 A 141 ILE LYS LYS MET ARG ASP LYS LEU THR LYS LEU ILE ARG SEQRES 10 A 141 LYS ALA LYS GLU LEU LEU ASP ARG LEU LYS LYS LYS ALA SEQRES 11 A 141 LYS LYS VAL GLN ASP GLU THR SER GLY GLY TRP SEQRES 1 B 141 MET GLU GLU GLU VAL ARG GLU LYS LEU LYS ARG MET GLU SEQRES 2 B 141 LYS LYS PHE ASP ASP SER LEU GLU LYS ALA GLU ARG LYS SEQRES 3 B 141 ILE ARG GLU ILE ILE LYS GLU ALA GLU LYS LYS LEU LYS SEQRES 4 B 141 THR LEU LYS LYS ARG ASN GLY PRO TYR GLU ALA VAL VAL SEQRES 5 B 141 THR THR LEU ARG ALA ILE LEU LYS ALA VAL GLU THR LYS SEQRES 6 B 141 ILE ARG ALA ILE ILE LYS ALA LEU LYS THR GLU LEU ASP SEQRES 7 B 141 ALA LEU ILE LYS ALA MET GLU THR ILE LEU LYS ALA HIS SEQRES 8 B 141 ASP LYS ASN ASP GLU LEU LYS LYS GLU VAL GLU ASP ILE SEQRES 9 B 141 ILE LYS LYS MET ARG ASP LYS LEU THR LYS LEU ILE ARG SEQRES 10 B 141 LYS ALA LYS GLU LEU LEU ASP ARG LEU LYS LYS LYS ALA SEQRES 11 B 141 LYS LYS VAL GLN ASP GLU THR SER GLY GLY TRP HELIX 1 AA1 GLU A 4 ASN A 45 1 42 HELIX 2 AA2 PRO A 47 HIS A 91 1 45 HELIX 3 AA3 GLU A 96 THR A 137 1 42 HELIX 4 AA4 GLU B 4 ASN B 45 1 42 HELIX 5 AA5 PRO B 47 ASP B 92 1 46 HELIX 6 AA6 LEU B 97 THR B 137 1 41 CRYST1 54.582 67.427 74.326 90.00 90.00 90.00 P 21 21 21 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 0.018321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013454 0.00000