HEADER DE NOVO PROTEIN 29-JAN-25 9N2Y TITLE CRYSTAL STRUCTURE OF LM1843 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LM1843; 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; 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 9N2Y 0 JRNL AUTH L.MILLES,A.K.BERA,D.BAKER JRNL TITL CRYSTAL STRUCTURE OF LM1843 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10968 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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 38.1900 - 2.9200 1.00 2723 147 0.1858 0.2292 REMARK 3 2 2.9200 - 2.3200 1.00 2633 108 0.2281 0.2241 REMARK 3 3 2.3200 - 2.0300 1.00 2580 131 0.2349 0.2959 REMARK 3 4 2.0200 - 1.8400 0.98 2513 133 0.2649 0.3274 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) : 0.228 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.757 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.64 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 : 0.010 1089 REMARK 3 ANGLE : 0.968 1468 REMARK 3 CHIRALITY : 0.058 168 REMARK 3 PLANARITY : 0.006 187 REMARK 3 DIHEDRAL : 22.043 416 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -19.7436 1.5382 -4.6424 REMARK 3 T TENSOR REMARK 3 T11: 0.2096 T22: 0.1884 REMARK 3 T33: 0.1986 T12: 0.0102 REMARK 3 T13: -0.0015 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 2.1266 L22: 1.8016 REMARK 3 L33: 2.6808 L12: 0.1848 REMARK 3 L13: -0.0731 L23: 0.2475 REMARK 3 S TENSOR REMARK 3 S11: -0.0062 S12: -0.0060 S13: 0.0188 REMARK 3 S21: -0.0180 S22: 0.0502 S23: 0.0274 REMARK 3 S31: 0.0273 S32: 0.0912 S33: -0.0340 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 9N2Y 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_1000292220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 11012 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 60.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.47100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 2.73800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M ZINC SULFATE, 0.1 M MES PH 6.5, REMARK 280 25 % PEG 550 MME, 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 20.33950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.07850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.71200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.07850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.33950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.71200 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 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 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 132 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 132 1.37 REMARK 500 O HOH A 305 O HOH A 306 2.09 REMARK 500 O HOH A 326 O HOH A 342 2.09 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 OH TYR A 29 NZ LYS A 37 4555 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 64 OE2 REMARK 620 2 GLU A 83 OE2 109.9 REMARK 620 3 HIS A 110 NE2 99.2 103.3 REMARK 620 4 GLU A 113 OE1 110.0 8.6 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 70 OD1 REMARK 620 2 ASP A 70 OD2 56.8 REMARK 620 3 GLU A 94 OE2 114.9 58.3 REMARK 620 4 HIS A 126 ND1 157.7 101.1 43.8 REMARK 620 5 HOH A 333 O 85.0 113.0 115.8 109.2 REMARK 620 N 1 2 3 4 DBREF 9N2Y A 1 134 PDB 9N2Y 9N2Y 1 134 SEQRES 1 A 134 GLY GLN ILE THR ILE GLU LYS SER PHE ASP GLY LYS PHE SEQRES 2 A 134 VAL GLY SER LYS THR ILE THR LEU GLN ASP ARG ASP PHE SEQRES 3 A 134 ALA SER TYR LEU GLU VAL THR VAL ASP GLY LYS PRO VAL SEQRES 4 A 134 ARG VAL TYR PHE LEU PHE ILE ASN ASN GLY ASN THR LEU SEQRES 5 A 134 THR LEU VAL GLU THR ALA THR ALA SER GLY TYR GLU ALA SEQRES 6 A 134 ASN SER MET THR ASP LYS THR THR GLY LYS LYS SER GLU SEQRES 7 A 134 LYS ILE PRO GLU GLU LYS LYS GLN GLU ILE ILE ASP LYS SEQRES 8 A 134 TYR LYS GLU ILE ALA LYS GLU GLN GLY LEU PRO GLU LEU SEQRES 9 A 134 ASP PRO GLU THR GLU HIS TRP THR GLU ASN LEU TYR SER SEQRES 10 A 134 LEU THR ILE ASP LEU ASP LYS ASN HIS THR ILE LYS ILE SEQRES 11 A 134 ASP ASN LYS LYS HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *42(H2 O) HELIX 1 AA1 PRO A 81 GLY A 100 1 20 SHEET 1 AA1 4 LYS A 12 THR A 20 0 SHEET 2 AA1 4 GLN A 2 PHE A 9 -1 N ILE A 3 O ILE A 19 SHEET 3 AA1 4 HIS A 126 LYS A 133 1 O ILE A 130 N GLU A 6 SHEET 4 AA1 4 GLU A 64 ASP A 70 -1 N THR A 69 O LYS A 129 SHEET 1 AA2 5 PHE A 26 VAL A 34 0 SHEET 2 AA2 5 LYS A 37 ASN A 47 -1 O PHE A 45 N PHE A 26 SHEET 3 AA2 5 THR A 51 ALA A 60 -1 O THR A 53 N ILE A 46 SHEET 4 AA2 5 TYR A 116 ASP A 121 -1 O LEU A 118 N LEU A 54 SHEET 5 AA2 5 GLU A 78 LYS A 79 -1 N GLU A 78 O SER A 117 SHEET 1 AA3 4 PHE A 26 VAL A 34 0 SHEET 2 AA3 4 LYS A 37 ASN A 47 -1 O PHE A 45 N PHE A 26 SHEET 3 AA3 4 THR A 51 ALA A 60 -1 O THR A 53 N ILE A 46 SHEET 4 AA3 4 GLU A 109 TRP A 111 -1 O HIS A 110 N THR A 59 LINK OE2 GLU A 64 ZN ZN A 202 1555 1555 1.74 LINK OD1 ASP A 70 ZN ZN A 201 1555 1555 2.56 LINK OD2 ASP A 70 ZN ZN A 201 1555 1555 1.83 LINK OE2 GLU A 83 ZN ZN A 202 1555 4545 1.83 LINK OE2 GLU A 94 ZN ZN A 201 1555 2455 1.91 LINK NE2 HIS A 110 ZN ZN A 202 1555 1555 2.17 LINK OE1 GLU A 113 ZN ZN A 202 1555 1555 1.95 LINK ND1 HIS A 126 ZN ZN A 201 1555 1555 2.22 LINK ZN ZN A 201 O HOH A 333 1555 1555 2.20 CRYST1 40.679 49.424 60.157 90.00 90.00 90.00 P 21 21 21 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 0.024583 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016623 0.00000 CONECT 499 1075 CONECT 540 1074 CONECT 541 1074 CONECT 868 1075 CONECT 897 1075 CONECT 1003 1074 CONECT 1074 540 541 1003 1108 CONECT 1075 499 868 897 CONECT 1108 1074 MASTER 266 0 2 1 13 0 0 6 1116 1 9 11 END