HEADER DE NOVO PROTEIN 29-JAN-25 9N2X TITLE CRYSTAL STRUCTURE OF LM1841 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LM1841; 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 PROTEIN, DESIGN MODEL, ISOPEPTIDE, ML/AI EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,L.MILLES,D.BAKER REVDAT 1 29-JUL-26 9N2X 0 JRNL AUTH L.MILLES,A.K.BERA,D.BAKER JRNL TITL CRYSTAL STRUCTURE OF LM1841 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 25912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1282 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 41.8600 - 3.7700 0.83 2560 152 0.1773 0.2034 REMARK 3 2 3.7600 - 2.9900 0.87 2672 142 0.1838 0.2462 REMARK 3 3 2.9900 - 2.6100 0.88 2722 136 0.2286 0.3324 REMARK 3 4 2.6100 - 2.3700 0.90 2734 155 0.2136 0.2557 REMARK 3 5 2.3700 - 2.2000 0.90 2802 109 0.2050 0.2701 REMARK 3 6 2.2000 - 2.0700 0.89 2708 159 0.2394 0.3234 REMARK 3 7 2.0700 - 1.9700 0.91 2789 146 0.2716 0.3297 REMARK 3 8 1.9700 - 1.8800 0.92 2792 152 0.3222 0.3651 REMARK 3 9 1.8800 - 1.8100 0.92 2851 131 0.4244 0.4580 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) : 0.299 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.761 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.82 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 : 0.008 2274 REMARK 3 ANGLE : 0.909 3106 REMARK 3 CHIRALITY : 0.059 378 REMARK 3 PLANARITY : 0.007 386 REMARK 3 DIHEDRAL : 12.731 806 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:143) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6016 3.1711 16.7991 REMARK 3 T TENSOR REMARK 3 T11: 0.2368 T22: 0.2657 REMARK 3 T33: 0.2861 T12: 0.0148 REMARK 3 T13: -0.0411 T23: 0.0306 REMARK 3 L TENSOR REMARK 3 L11: 3.4341 L22: 8.0068 REMARK 3 L33: 2.1954 L12: 0.5426 REMARK 3 L13: -0.7102 L23: 0.5014 REMARK 3 S TENSOR REMARK 3 S11: -0.0617 S12: 0.2043 S13: 0.1856 REMARK 3 S21: -0.4178 S22: 0.1241 S23: 0.0052 REMARK 3 S31: 0.2423 S32: 0.0262 S33: -0.0471 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 1:143) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1893 -22.2455 23.4080 REMARK 3 T TENSOR REMARK 3 T11: 0.2563 T22: 0.2572 REMARK 3 T33: 0.2456 T12: 0.0048 REMARK 3 T13: 0.0546 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 4.0795 L22: 7.1970 REMARK 3 L33: 2.1827 L12: -0.5985 REMARK 3 L13: 0.5672 L23: -0.3127 REMARK 3 S TENSOR REMARK 3 S11: -0.1445 S12: -0.2830 S13: -0.0667 REMARK 3 S21: 0.2313 S22: 0.1305 S23: 0.0196 REMARK 3 S31: -0.1271 S32: 0.0313 S33: 0.0098 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 9N2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292219. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 41.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07890 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.98400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.870 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 (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS REMARK 280 PH 8.5, 3.4 M 1,6-HEXANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 54.25050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 ASN A 141 ND2 REMARK 470 ASN B 141 ND2 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 NZ LYS A 7 CG ASN A 141 1.38 REMARK 500 NZ LYS B 7 CG ASN B 141 1.43 REMARK 500 O HOH B 204 O HOH B 234 1.92 REMARK 500 O HOH B 218 O HOH B 244 2.11 REMARK 500 O HOH B 233 O HOH B 238 2.12 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 ALA B 10 34.98 -88.29 REMARK 500 PHE B 15 109.91 -48.87 REMARK 500 LYS B 32 61.35 -156.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 9N2X A 1 143 PDB 9N2X 9N2X 1 143 DBREF 9N2X B 1 143 PDB 9N2X 9N2X 1 143 SEQRES 1 A 143 LYS LYS ILE THR VAL ASN LYS THR TRP ALA GLU THR LEU SEQRES 2 A 143 THR PHE LYS SER TYR SER VAL SER LYS PHE ARG ASN GLY SEQRES 3 A 143 LYS GLU VAL PRO LEU LYS PRO GLU ASP TYR SER VAL SER SEQRES 4 A 143 ALA THR ALA ASN THR ASP VAL THR SER PHE THR VAL THR SEQRES 5 A 143 ALA VAL LEU GLU ASP ASN GLU THR PHE VAL PHE LYS ALA SEQRES 6 A 143 THR PHE GLU LYS ASP GLY LYS THR TYR GLU LEU THR ILE SEQRES 7 A 143 THR VAL THR LYS THR PRO ASP GLY VAL THR VAL ILE GLU SEQRES 8 A 143 ARG VAL SER GLY TYR ALA PRO GLU PHE THR SER ALA THR SEQRES 9 A 143 LEU ASP GLY GLN PRO TYR THR VAL THR GLN THR THR TRP SEQRES 10 A 143 SER SER ASN GLY TYR ASN TYR ALA SER ILE THR LEU PRO SEQRES 11 A 143 ALA ALA GLU ASN ILE THR VAL THR ILE LYS ASN ASN LYS SEQRES 1 B 143 LYS LYS ILE THR VAL ASN LYS THR TRP ALA GLU THR LEU SEQRES 2 B 143 THR PHE LYS SER TYR SER VAL SER LYS PHE ARG ASN GLY SEQRES 3 B 143 LYS GLU VAL PRO LEU LYS PRO GLU ASP TYR SER VAL SER SEQRES 4 B 143 ALA THR ALA ASN THR ASP VAL THR SER PHE THR VAL THR SEQRES 5 B 143 ALA VAL LEU GLU ASP ASN GLU THR PHE VAL PHE LYS ALA SEQRES 6 B 143 THR PHE GLU LYS ASP GLY LYS THR TYR GLU LEU THR ILE SEQRES 7 B 143 THR VAL THR LYS THR PRO ASP GLY VAL THR VAL ILE GLU SEQRES 8 B 143 ARG VAL SER GLY TYR ALA PRO GLU PHE THR SER ALA THR SEQRES 9 B 143 LEU ASP GLY GLN PRO TYR THR VAL THR GLN THR THR TRP SEQRES 10 B 143 SER SER ASN GLY TYR ASN TYR ALA SER ILE THR LEU PRO SEQRES 11 B 143 ALA ALA GLU ASN ILE THR VAL THR ILE LYS ASN ASN LYS FORMUL 3 HOH *92(H2 O) SHEET 1 AA112 GLN A 108 PRO A 109 0 SHEET 2 AA112 ALA A 97 LEU A 105 -1 N LEU A 105 O GLN A 108 SHEET 3 AA112 ASN A 134 ASN A 142 -1 O THR A 138 N THR A 101 SHEET 4 AA112 LYS A 2 TRP A 9 1 N THR A 8 O ASN A 141 SHEET 5 AA112 THR A 47 VAL A 54 -1 O PHE A 49 N LYS A 7 SHEET 6 AA112 TYR A 36 ALA A 42 -1 N THR A 41 O SER A 48 SHEET 7 AA112 TYR B 36 ALA B 42 -1 O VAL B 38 N ALA A 40 SHEET 8 AA112 THR B 47 VAL B 54 -1 O SER B 48 N THR B 41 SHEET 9 AA112 LYS B 2 TRP B 9 -1 N LYS B 7 O PHE B 49 SHEET 10 AA112 ASN B 134 ASN B 142 1 O VAL B 137 N THR B 4 SHEET 11 AA112 ALA B 97 LEU B 105 -1 N ALA B 97 O ASN B 142 SHEET 12 AA112 GLN B 108 TYR B 110 -1 O TYR B 110 N ALA B 103 SHEET 1 AA2 4 LYS A 27 VAL A 29 0 SHEET 2 AA2 4 THR A 14 ARG A 24 -1 N ARG A 24 O LYS A 27 SHEET 3 AA2 4 THR B 14 ARG B 24 -1 O TYR B 18 N TYR A 18 SHEET 4 AA2 4 LYS B 27 VAL B 29 -1 O LYS B 27 N ARG B 24 SHEET 1 AA312 GLN A 114 SER A 119 0 SHEET 2 AA312 TYR A 122 LEU A 129 -1 O TYR A 124 N TRP A 117 SHEET 3 AA312 GLY A 86 VAL A 93 -1 N VAL A 87 O LEU A 129 SHEET 4 AA312 LYS A 72 THR A 83 -1 N THR A 77 O ARG A 92 SHEET 5 AA312 GLU A 59 LYS A 69 -1 N PHE A 67 O TYR A 74 SHEET 6 AA312 THR A 14 ARG A 24 -1 N SER A 19 O LYS A 64 SHEET 7 AA312 THR B 14 ARG B 24 -1 O TYR B 18 N TYR A 18 SHEET 8 AA312 GLU B 59 LYS B 69 -1 O THR B 66 N LYS B 16 SHEET 9 AA312 LYS B 72 THR B 83 -1 O ILE B 78 N PHE B 63 SHEET 10 AA312 GLY B 86 VAL B 93 -1 O THR B 88 N THR B 81 SHEET 11 AA312 TYR B 122 LEU B 129 -1 O ASN B 123 N VAL B 93 SHEET 12 AA312 THR B 115 SER B 119 -1 N TRP B 117 O TYR B 124 CRYST1 35.765 108.501 45.450 90.00 112.91 90.00 P 1 21 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 0.027960 0.000000 0.011819 0.00000 SCALE2 0.000000 0.009217 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023887 0.00000 MASTER 267 0 0 0 28 0 0 6 2320 2 0 22 END