HEADER DE NOVO PROTEIN 31-JAN-24 8VW7 TITLE UIC-11-BPE-AGNO3 SILVER BINDING WITH UIC-11-BPE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-11-BPE-AGNO3; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC CONSTRUCT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.GANATRA REVDAT 3 04-SEP-24 8VW7 1 JRNL REVDAT 2 14-AUG-24 8VW7 1 JRNL REVDAT 1 07-AUG-24 8VW7 0 JRNL AUTH P.GANATRA,D.F.WANG,V.GANATRA,V.T.DANG,A.I.NGUYEN JRNL TITL DIVERSE PROTEOMIMETIC FRAMEWORKS VIA RATIONAL DESIGN OF JRNL TITL 2 PI-STACKING PEPTIDE TECTONS. JRNL REF J.AM.CHEM.SOC. V. 146 22236 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 39096501 JRNL DOI 10.1021/JACS.4C03094 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 6790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1343 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 17.3100 - 2.8000 0.88 1183 123 0.1584 0.1904 REMARK 3 2 2.8000 - 2.2200 0.92 1226 140 0.1799 0.2555 REMARK 3 3 2.2200 - 1.9400 0.92 1237 142 0.2227 0.2073 REMARK 3 4 1.9400 - 1.7600 0.83 1049 122 0.2655 0.2352 REMARK 3 5 1.7600 - 1.6400 0.89 1273 149 0.2539 0.2971 REMARK 3 6 1.6400 - 1.5400 0.89 1143 121 0.2913 0.3526 REMARK 3 7 1.5400 - 1.4600 0.92 1237 134 0.2953 0.3542 REMARK 3 8 1.4600 - 1.4000 0.93 1274 147 0.3243 0.3384 REMARK 3 9 1.4000 - 1.3500 0.84 1109 140 0.3180 0.3075 REMARK 3 10 1.3500 - 1.3000 0.82 1064 125 0.3458 0.3765 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.769 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 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 : 0.009 230 REMARK 3 ANGLE : 2.008 324 REMARK 3 CHIRALITY : 0.042 18 REMARK 3 PLANARITY : 0.008 38 REMARK 3 DIHEDRAL : 34.392 62 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 8VW7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-23 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.619900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6790 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 17.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 62.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETONITRILE, WATER, SLOW COOLING, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 AG A 103 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I6W A 1 N10 REMARK 620 2 I6W A 1 N07 71.6 REMARK 620 3 I77 B 13 N07 31.0 44.7 REMARK 620 4 I77 B 13 N10 33.2 40.8 4.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 101 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I77 A 13 N07 REMARK 620 2 I77 A 13 N10 70.4 REMARK 620 3 I6W B 1 N10 117.3 76.7 REMARK 620 4 I6W B 1 N07 126.2 70.0 17.7 REMARK 620 N 1 2 3 DBREF 8VW7 A 1 13 PDB 8VW7 8VW7 1 13 DBREF 8VW7 B 1 13 PDB 8VW7 8VW7 1 13 SEQRES 1 A 13 I6W ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 SEQRES 1 B 13 I6W ALA AIB LEU AIB ALA AIB LEU AIB GLN AIB LEU I77 HET I6W A 1 30 HET AIB A 3 13 HET AIB A 5 13 HET AIB A 7 13 HET AIB A 9 13 HET AIB A 11 13 HET I77 A 13 29 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 5 13 HET AIB B 7 13 HET AIB B 9 13 HET AIB B 11 13 HET I77 B 13 29 HET AG A 101 1 HET NO3 A 102 4 HET AG A 103 1 HET NO3 B 101 4 HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE HETNAM AG SILVER ION HETNAM NO3 NITRATE ION FORMUL 1 I6W 2(C14 H12 N2 O3) FORMUL 1 AIB 10(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 AG 2(AG 1+) FORMUL 4 NO3 2(N O3 1-) FORMUL 7 HOH *15(H2 O) HELIX 1 AA1 ALA A 2 LEU A 12 1 11 HELIX 2 AA2 AIB B 3 LEU B 12 1 10 LINK C02 I6W A 1 N ALA A 2 1555 1555 1.43 LINK C ALA A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N LEU A 4 1555 1555 1.33 LINK C LEU A 4 N AIB A 5 1555 1555 1.32 LINK C AIB A 5 N ALA A 6 1555 1555 1.33 LINK C ALA A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N LEU A 8 1555 1555 1.33 LINK C LEU A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N GLN A 10 1555 1555 1.33 LINK C GLN A 10 N AIB A 11 1555 1555 1.33 LINK C AIB A 11 N LEU A 12 1555 1555 1.33 LINK C LEU A 12 N15 I77 A 13 1555 1555 1.43 LINK C02 I6W B 1 N ALA B 2 1555 1555 1.43 LINK C ALA B 2 N AIB B 3 1555 1555 1.32 LINK C AIB B 3 N LEU B 4 1555 1555 1.33 LINK C LEU B 4 N AIB B 5 1555 1555 1.33 LINK C AIB B 5 N ALA B 6 1555 1555 1.33 LINK C ALA B 6 N AIB B 7 1555 1555 1.33 LINK C AIB B 7 N LEU B 8 1555 1555 1.33 LINK C LEU B 8 N AIB B 9 1555 1555 1.33 LINK C AIB B 9 N GLN B 10 1555 1555 1.32 LINK C GLN B 10 N AIB B 11 1555 1555 1.33 LINK C AIB B 11 N LEU B 12 1555 1555 1.33 LINK C LEU B 12 N15 I77 B 13 1555 1555 1.43 LINK N10 I6W A 1 AG AG A 103 1555 1554 2.36 LINK N07 I6W A 1 AG AG A 103 1555 1554 2.39 LINK N07 I77 A 13 AG AG A 101 1555 1456 2.33 LINK N10 I77 A 13 AG AG A 101 1555 1456 2.29 LINK AG AG A 101 N10 I6W B 1 1556 1555 2.34 LINK AG AG A 101 N07 I6W B 1 1556 1555 2.44 LINK AG AG A 103 N07 I77 B 13 1665 1555 2.34 LINK AG AG A 103 N10 I77 B 13 1665 1555 2.23 CRYST1 9.025 30.416 30.437 110.65 90.13 90.07 P 1 2 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 0.110803 0.000135 0.000320 0.00000 SCALE2 0.000000 0.032877 0.012391 0.00000 SCALE3 0.000000 0.000000 0.035111 0.00000 HETATM 1 C05 I6W A 1 3.026 1.837 -7.177 1.00 32.81 C ANISOU 1 C05 I6W A 1 6692 2742 3034 -185 111 1195 C HETATM 2 C08 I6W A 1 2.774 1.856 -8.519 1.00 31.53 C ANISOU 2 C08 I6W A 1 5875 2897 3208 -226 386 1396 C HETATM 3 C09 I6W A 1 2.691 3.166 -9.304 1.00 35.38 C ANISOU 3 C09 I6W A 1 6691 3198 3553 -90 317 1669 C HETATM 4 N10 I6W A 1 2.788 3.107 -10.606 1.00 37.47 N ANISOU 4 N10 I6W A 1 7116 3344 3776 -238 50 1755 N HETATM 5 C02 I6W A 1 3.048 -1.885 -6.495 1.00 23.97 C ANISOU 5 C02 I6W A 1 4039 2450 2619 -655 275 752 C HETATM 6 C03 I6W A 1 2.954 -0.538 -7.233 1.00 27.06 C ANISOU 6 C03 I6W A 1 4981 2520 2780 -252 38 998 C HETATM 7 C04 I6W A 1 3.111 0.613 -6.492 1.00 32.05 C ANISOU 7 C04 I6W A 1 6586 2597 2996 -215 -84 1109 C HETATM 8 C06 I6W A 1 2.726 -0.453 -8.599 1.00 23.17 C ANISOU 8 C06 I6W A 1 3408 2569 2828 -256 234 1054 C HETATM 9 C11 I6W A 1 2.743 4.171 -11.380 1.00 37.14 C ANISOU 9 C11 I6W A 1 6837 3429 3846 -22 -44 1654 C HETATM 10 C12 I6W A 1 2.596 5.421 -10.811 1.00 38.00 C ANISOU 10 C12 I6W A 1 6873 3576 3991 119 68 1681 C HETATM 11 C13 I6W A 1 2.555 6.686 -11.717 1.00 37.43 C ANISOU 11 C13 I6W A 1 6213 3630 4380 -85 -419 1543 C HETATM 12 C15 I6W A 1 1.697 8.737 -11.024 1.00 37.09 C ANISOU 12 C15 I6W A 1 6084 3810 4198 642 1400 1053 C HETATM 13 C16 I6W A 1 2.066 10.170 -10.584 1.00 38.39 C ANISOU 13 C16 I6W A 1 6626 3955 4004 818 1564 844 C HETATM 14 C18 I6W A 1 2.498 5.543 -9.445 1.00 36.54 C ANISOU 14 C18 I6W A 1 6531 3523 3828 501 769 1758 C HETATM 15 C19 I6W A 1 2.548 4.385 -8.674 1.00 35.49 C ANISOU 15 C19 I6W A 1 6562 3302 3619 321 794 1624 C HETATM 16 N07 I6W A 1 2.646 0.726 -9.192 1.00 26.83 N ANISOU 16 N07 I6W A 1 4489 2721 2983 -262 499 1134 N HETATM 17 O01 I6W A 1 2.933 -1.881 -5.300 1.00 23.74 O ANISOU 17 O01 I6W A 1 3891 2543 2588 -548 674 695 O HETATM 18 O14 I6W A 1 2.880 7.937 -11.137 1.00 39.33 O ANISOU 18 O14 I6W A 1 6972 3684 4289 268 575 1294 O HETATM 19 O17 I6W A 1 2.264 6.604 -12.852 1.00 33.85 O ANISOU 19 O17 I6W A 1 4542 3577 4744 -646 -1348 1561 O HETATM 20 H051 I6W A 1 3.159 2.755 -6.647 1.00 39.42 H HETATM 21 H041 I6W A 1 3.299 0.574 -5.388 1.00 38.51 H HETATM 22 H061 I6W A 1 2.613 -1.361 -9.184 1.00 27.85 H HETATM 23 H111 I6W A 1 2.820 4.069 -12.437 1.00 44.61 H HETATM 24 H152 I6W A 1 1.036 8.297 -10.288 1.00 44.55 H HETATM 25 H151 I6W A 1 1.198 8.776 -11.984 1.00 44.55 H HETATM 26 H162 I6W A 1 2.552 10.136 -9.591 1.00 46.10 H HETATM 27 H163 I6W A 1 1.148 10.785 -10.525 1.00 46.10 H HETATM 28 H161 I6W A 1 2.761 10.614 -11.321 1.00 46.10 H HETATM 29 H181 I6W A 1 2.385 6.521 -8.976 1.00 43.89 H HETATM 30 H191 I6W A 1 2.476 4.440 -7.590 1.00 42.62 H