HEADER DE NOVO PROTEIN 01-DEC-23 8V5W TITLE UIC-1 MUTANT UIC-1-B5T COMPND MOL_ID: 1; COMPND 2 MOLECULE: UIC-1-B5T; 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 S.L.HEINZ-KUNERT REVDAT 2 20-MAR-24 8V5W 1 JRNL REVDAT 1 06-MAR-24 8V5W 0 JRNL AUTH S.L.HEINZ-KUNERT,A.PANDYA,V.T.DANG,J.OKTAWIEC,A.I.NGUYEN JRNL TITL PORE RESTRUCTURING OF PEPTIDE FRAMEWORKS BY MUTATIONS AT JRNL TITL 2 DISTAL PACKING RESIDUES. JRNL REF BIOMACROMOLECULES V. 25 2016 2024 JRNL REFN ESSN 1526-4602 JRNL PMID 38362872 JRNL DOI 10.1021/ACS.BIOMAC.3C01418 REMARK 2 REMARK 2 RESOLUTION. 1.07 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 7816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1425 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 22.3900 - 2.3100 0.96 1319 140 0.1536 0.1873 REMARK 3 2 2.3000 - 1.8300 0.99 1346 150 0.1529 0.1852 REMARK 3 3 1.8300 - 1.6000 0.98 1347 149 0.0000 0.1554 REMARK 3 4 1.6000 - 1.4500 0.94 1238 142 0.0000 0.1462 REMARK 3 5 1.4500 - 1.3500 0.96 1335 147 0.1653 0.1762 REMARK 3 6 1.3500 - 1.2700 0.98 1296 144 0.1494 0.1775 REMARK 3 7 1.2700 - 1.2100 0.99 1396 150 0.1565 0.1674 REMARK 3 8 1.2100 - 1.1500 0.98 1317 149 0.1626 0.1920 REMARK 3 9 1.1500 - 1.1100 0.90 1231 137 0.1813 0.1993 REMARK 3 10 1.1100 - 1.0700 0.75 1026 117 0.1935 0.2120 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) : 0.077 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.596 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.68 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 : 0.009 222 REMARK 3 ANGLE : 1.755 310 REMARK 3 CHIRALITY : 0.046 23 REMARK 3 PLANARITY : 0.011 36 REMARK 3 DIHEDRAL : 39.407 39 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 8V5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.61992 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 : 7816 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 22.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38450 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.450 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 (%): 22.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, SLOW COOLING, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.97800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 5.08200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.97800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 5.08200 REMARK 290 SMTRY3 4 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 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 O HOH A 103 O HOH A 109 2.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 8V5W A 1 11 PDB 8V5W 8V5W 1 11 DBREF 8V5W B 1 11 PDB 8V5W 8V5W 1 11 SEQRES 1 A 11 I6W LEU AIB ALA THR LEU AIB GLN AIB LEU I77 SEQRES 1 B 11 I6W LEU AIB ALA THR LEU AIB GLN AIB LEU I77 HET I6W A 1 30 HET AIB A 3 13 HET AIB A 7 13 HET AIB A 9 13 HET I77 A 11 29 HET I6W B 1 30 HET AIB B 3 13 HET AIB B 7 13 HET AIB B 9 13 HET I77 B 11 29 HETNAM I6W ETHYL 5'-FORMYL[2,2'-BIPYRIDINE]-5-CARBOXYLATE HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM I77 5'-(HYDRAZINECARBONYL)[2,2'-BIPYRIDINE]-5-CARBOXAMIDE FORMUL 1 I6W 2(C14 H12 N2 O3) FORMUL 1 AIB 6(C4 H9 N O2) FORMUL 1 I77 2(C12 H11 N5 O2) FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 LEU A 2 GLN A 8 1 7 HELIX 2 AA2 AIB B 3 GLN B 8 1 6 LINK C02 I6W A 1 N LEU A 2 1555 1555 1.42 LINK C LEU A 2 N AIB A 3 1555 1555 1.33 LINK C AIB A 3 N ALA A 4 1555 1555 1.33 LINK C LEU A 6 N AIB A 7 1555 1555 1.33 LINK C AIB A 7 N GLN A 8 1555 1555 1.33 LINK C GLN A 8 N AIB A 9 1555 1555 1.33 LINK C AIB A 9 N LEU A 10 1555 1555 1.34 LINK C LEU A 10 N15 I77 A 11 1555 1555 1.42 LINK C02 I6W B 1 N LEU B 2 1555 1555 1.42 LINK C LEU B 2 N AIB B 3 1555 1555 1.32 LINK C AIB B 3 N ALA B 4 1555 1555 1.34 LINK C LEU B 6 N AIB B 7 1555 1555 1.33 LINK C AIB B 7 N AGLN B 8 1555 1555 1.33 LINK C AIB B 7 N BGLN B 8 1555 1555 1.33 LINK C AGLN B 8 N AIB B 9 1555 1555 1.33 LINK C BGLN B 8 N AIB B 9 1555 1555 1.33 LINK C AIB B 9 N ALEU B 10 1555 1555 1.34 LINK C AIB B 9 N BLEU B 10 1555 1555 1.33 LINK C ALEU B 10 N15 I77 B 11 1555 1555 1.42 LINK C BLEU B 10 N15 I77 B 11 1555 1555 1.43 CRYST1 53.956 10.164 32.761 90.00 99.18 90.00 C 1 2 1 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 0.018534 0.000000 0.002995 0.00000 SCALE2 0.000000 0.098386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030920 0.00000 HETATM 1 C05 I6W A 1 19.009 -6.728 25.032 1.00 4.58 C ANISOU 1 C05 I6W A 1 495 579 665 15 -150 -38 C HETATM 2 C08 I6W A 1 20.306 -6.810 24.616 1.00 4.82 C ANISOU 2 C08 I6W A 1 509 567 755 14 -255 29 C HETATM 3 C09 I6W A 1 21.436 -6.752 25.610 1.00 6.29 C ANISOU 3 C09 I6W A 1 581 970 840 20 -305 97 C HETATM 4 N10 I6W A 1 21.189 -6.539 26.880 1.00 8.93 N ANISOU 4 N10 I6W A 1 676 1798 917 116 -311 44 N HETATM 5 C02 I6W A 1 17.353 -7.074 21.619 1.00 5.00 C ANISOU 5 C02 I6W A 1 564 759 577 -13 -189 38 C HETATM 6 C03 I6W A 1 18.359 -6.966 22.758 1.00 4.70 C ANISOU 6 C03 I6W A 1 539 568 678 -14 -199 18 C HETATM 7 C04 I6W A 1 17.975 -6.805 24.084 1.00 4.56 C ANISOU 7 C04 I6W A 1 535 528 669 47 -141 -86 C HETATM 8 C06 I6W A 1 19.685 -7.039 22.421 1.00 5.29 C ANISOU 8 C06 I6W A 1 518 745 746 30 -208 5 C HETATM 9 C11 I6W A 1 22.173 -6.524 27.754 1.00 9.34 C ANISOU 9 C11 I6W A 1 719 1830 1000 98 -369 4 C HETATM 10 C12 I6W A 1 23.483 -6.752 27.346 1.00 8.58 C ANISOU 10 C12 I6W A 1 670 1520 1070 130 -425 33 C HETATM 11 C13 I6W A 1 24.617 -6.718 28.398 1.00 12.45 C ANISOU 11 C13 I6W A 1 881 2558 1291 223 -370 -72 C HETATM 12 C15 I6W A 1 25.270 -6.279 30.665 1.00 18.75 C ANISOU 12 C15 I6W A 1 1240 4320 1564 358 -243 -278 C HETATM 13 C16 I6W A 1 25.076 -4.844 31.208 1.00 20.76 C ANISOU 13 C16 I6W A 1 1354 4859 1674 350 -222 -272 C HETATM 14 C18 I6W A 1 23.769 -6.994 26.035 1.00 6.73 C ANISOU 14 C18 I6W A 1 605 982 972 6 -381 -162 C HETATM 15 C19 I6W A 1 22.707 -6.997 25.149 1.00 6.39 C ANISOU 15 C19 I6W A 1 584 942 901 -101 -351 -61 C HETATM 16 N07 I6W A 1 20.629 -6.968 23.340 1.00 5.26 N ANISOU 16 N07 I6W A 1 491 763 744 12 -175 162 N HETATM 17 O01 I6W A 1 17.638 -6.807 20.482 1.00 5.34 O ANISOU 17 O01 I6W A 1 625 919 486 -58 -144 104 O HETATM 18 O14 I6W A 1 24.205 -6.500 29.730 1.00 16.43 O ANISOU 18 O14 I6W A 1 1103 3691 1451 244 -284 -340 O HETATM 19 O17 I6W A 1 25.741 -6.862 28.095 1.00 13.10 O ANISOU 19 O17 I6W A 1 901 2766 1311 264 -326 -101 O HETATM 20 H051 I6W A 1 18.783 -6.605 26.069 1.00 5.49 H HETATM 21 H041 I6W A 1 16.898 -6.740 24.381 1.00 5.47 H HETATM 22 H061 I6W A 1 19.964 -7.158 21.378 1.00 6.34 H HETATM 23 H111 I6W A 1 21.965 -6.334 28.781 1.00 11.21 H HETATM 24 H152 I6W A 1 26.229 -6.365 30.168 1.00 22.50 H HETATM 25 H151 I6W A 1 25.214 -6.997 31.474 1.00 22.50 H HETATM 26 H162 I6W A 1 24.660 -4.202 30.409 1.00 24.91 H HETATM 27 H163 I6W A 1 26.051 -4.440 31.537 1.00 24.91 H HETATM 28 H161 I6W A 1 24.377 -4.866 32.064 1.00 24.91 H HETATM 29 H181 I6W A 1 24.790 -7.177 25.699 1.00 8.08 H HETATM 30 H191 I6W A 1 22.877 -7.193 24.092 1.00 7.67 H