HEADER DE NOVO PROTEIN 23-AUG-24 9DBU TITLE APO STRUCTURE OF COMPUTATIONALLY DESIGNED HOMOTETRAMER PW1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPUTATIONALLY DESIGNED PW1; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METALLOPROTEIN, COMPUTATIONAL DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.HOFFNAGLE,F.A.TEZCAN REVDAT 2 11-MAR-26 9DBU 1 JRNL REVDAT 1 27-AUG-25 9DBU 0 JRNL AUTH A.M.HOFFNAGLE,R.A.HEROLD,C.Y.TSAI,A.A.SHIAU,R.D.BRITT, JRNL AUTH 2 F.A.TEZCAN JRNL TITL DE NOVO DESIGN OF A METALLOPROTEIN WITH A SYNTHETICALLY JRNL TITL 2 INSPIRED DINUCLEAR PADDLEWHEEL COORDINATION MOTIF. JRNL REF J.AM.CHEM.SOC. V. 147 40788 2025 JRNL REFN ESSN 1520-5126 JRNL PMID 41143657 JRNL DOI 10.1021/JACS.5C13813 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9079 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) : 0.206 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 907 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 32.9200 - 3.0900 1.00 1407 161 0.1669 0.2038 REMARK 3 2 3.0800 - 2.4500 1.00 1343 148 0.2235 0.2559 REMARK 3 3 2.4500 - 2.1400 1.00 1360 154 0.2446 0.2612 REMARK 3 4 2.1400 - 1.9500 1.00 1347 146 0.2752 0.3038 REMARK 3 5 1.9500 - 1.8100 1.00 1346 147 0.3202 0.3970 REMARK 3 6 1.8100 - 1.7000 1.00 1369 151 0.3209 0.3253 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) : 0.315 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.812 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.48 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 : 0.004 802 REMARK 3 ANGLE : 0.753 1090 REMARK 3 CHIRALITY : 0.047 139 REMARK 3 PLANARITY : 0.004 144 REMARK 3 DIHEDRAL : 13.380 295 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): 3.8479 -15.1822 2.7117 REMARK 3 T TENSOR REMARK 3 T11: 0.2963 T22: 0.3024 REMARK 3 T33: 0.3150 T12: 0.0048 REMARK 3 T13: 0.0378 T23: 0.1355 REMARK 3 L TENSOR REMARK 3 L11: 5.4483 L22: 5.8098 REMARK 3 L33: 3.2839 L12: 0.0091 REMARK 3 L13: -0.3660 L23: -0.4940 REMARK 3 S TENSOR REMARK 3 S11: -0.1299 S12: -0.6534 S13: -0.8433 REMARK 3 S21: 0.6784 S22: -0.0847 S23: -0.2736 REMARK 3 S31: 0.0719 S32: 0.0570 S33: 0.1073 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 9DBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-23 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991840 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 32.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.05809 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 1.42300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.820 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 (%): 28.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 1500, 200 MM (NH4)2SO4, 100 MM REMARK 280 BIS-TRIS (PH 6.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.92000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.92000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.98500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.92000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.92000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.98500 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 32.92000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 32.92000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 18.98500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 32.92000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 32.92000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 18.98500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 224 LIES ON A SPECIAL POSITION. 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 ASN A 107 REMARK 465 LEU A 108 REMARK 465 TYR A 109 REMARK 465 PHE A 110 REMARK 465 GLN A 111 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 OE2 GLU A 53 NH2 ARG A 56 4555 2.02 REMARK 500 OE1 GLU A 52 OE2 GLU A 52 4555 2.04 REMARK 500 OE2 GLU A 16 O HOH A 210 1556 2.09 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 SER A 104 -108.75 58.53 REMARK 500 ALA A 105 -67.24 62.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 225 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 226 DISTANCE = 8.07 ANGSTROMS DBREF 9DBU A 1 111 PDB 9DBU 9DBU 1 111 SEQRES 1 A 111 SER THR ARG GLU GLU ALA LEU ARG GLU ALA GLU ARG LEU SEQRES 2 A 111 SER PRO GLU VAL ARG ARG ARG VAL ARG VAL ALA LEU LEU SEQRES 3 A 111 LEU ILE GLU LEU LEU ALA ALA ALA GLU GLN ALA GLY ASN SEQRES 4 A 111 THR ASN ILE ALA ASN ASN LEU ALA THR THR ILE ILE GLU SEQRES 5 A 111 GLU ALA ALA ARG ILE VAL LEU GLU PHE PRO ALA GLU ALA SEQRES 6 A 111 ALA GLU ALA PHE ARG ILE LEU ALA ARG ALA ALA ALA ALA SEQRES 7 A 111 GLN ALA ALA ALA THR LYS SER THR ILE LEU ALA ASN LEU SEQRES 8 A 111 ALA ALA LEU PHE ALA ARG ALA ALA GLU LEU LEU ALA SER SEQRES 9 A 111 ALA GLU ASN LEU TYR PHE GLN FORMUL 2 HOH *26(H2 O) HELIX 1 AA1 SER A 1 GLU A 11 1 11 HELIX 2 AA2 SER A 14 GLY A 38 1 25 HELIX 3 AA3 ASN A 39 PHE A 61 1 23 HELIX 4 AA4 PHE A 61 LYS A 84 1 24 HELIX 5 AA5 SER A 85 ALA A 103 1 19 CRYST1 65.840 65.840 37.970 90.00 90.00 90.00 I 4 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 0.015188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026337 0.00000 MASTER 312 0 0 5 0 0 0 6 816 1 0 9 END