HEADER DE NOVO PROTEIN 20-MAY-25 9RAA TITLE APO CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED PROTEIN (TRP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TANDEM-REPEAT PROTEIN (TRP); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 STRAIN: LEMO-21; SOURCE 5 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.F.MORRIS,T.R.WARD REVDAT 1 03-JUN-26 9RAA 0 JRNL AUTH E.F.MORRIS,T.R.WARD JRNL TITL CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED JRNL TITL 2 TANDEM-REPEAT PROTEIN (TRP) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 13445 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2564 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3087 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.3624 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : -2.52000 REMARK 3 B33 (A**2) : 2.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.832 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1602 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1755 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2171 ; 1.833 ; 1.876 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4032 ; 0.549 ; 1.739 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 215 ; 5.245 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ; 5.497 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;17.523 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 294 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1770 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 292 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 851 ; 3.776 ; 3.874 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 851 ; 3.775 ; 3.874 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1069 ; 5.070 ; 6.944 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1070 ; 5.068 ; 6.947 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 751 ; 4.897 ; 4.564 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 752 ; 4.894 ; 4.567 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1103 ; 7.429 ; 8.106 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1881 ; 8.902 ;38.860 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1871 ; 8.904 ;38.450 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9RAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1292147973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-25 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 60.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 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 (%): 52.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.76 MGML-1 TRP (IN 20 MM MES PH 5.2, REMARK 280 150 MM NACL) WAS PIPETTED INTO AN MRC 3-WELL PLATE IN A 1:2 REMARK 280 RATIO TRP:MOTHER LIQUOR, WHERE MOTHER LIQUOR = 1% (W/V) TRYPTONE, REMARK 280 0.05 M HEPES PH 7, 12% (W/V) PEG 3350. CRYSTALS GREW AFTER 1-2 REMARK 280 DAYS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 30.16500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 19 REMARK 465 GLY A 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 GLY A 23 REMARK 465 LEU A 232 REMARK 465 GLY A 233 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 48 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9RAA A 19 233 PDB 9RAA 9RAA 19 233 SEQRES 1 A 215 GLY GLY GLY SER GLY VAL SER LEU GLU GLN ALA LEU LEU SEQRES 2 A 215 ILE LEU SER VAL ALA ALA LEU LEU GLY THR THR VAL GLU SEQRES 3 A 215 GLU ALA VAL LYS ARG ALA LEU TRP LEU LYS THR LYS LEU SEQRES 4 A 215 GLY VAL SER LEU GLU GLN ALA ALA PHE ILE LEU SER VAL SEQRES 5 A 215 ALA ALA TYR LEU GLY THR THR VAL GLU GLU ALA VAL LYS SEQRES 6 A 215 ARG ALA LEU LYS LEU LYS THR LYS LEU GLY VAL SER LEU SEQRES 7 A 215 GLU GLN ALA LEU LEU ILE LEU PHE ALA ALA ALA ALA LEU SEQRES 8 A 215 GLY THR THR VAL GLU GLU ALA VAL LYS ARG ALA LEU LYS SEQRES 9 A 215 LEU LYS THR LYS LEU GLY VAL SER LEU GLU GLN ALA LEU SEQRES 10 A 215 LEU ILE LEU PHE THR ALA ALA GLU LEU GLY THR THR VAL SEQRES 11 A 215 GLU GLU ALA VAL LYS ARG ALA LEU LYS LEU LYS THR LYS SEQRES 12 A 215 LEU GLY VAL SER LEU GLU GLN ALA GLN ALA ILE LEU VAL SEQRES 13 A 215 VAL ALA ALA GLU LEU GLY THR THR VAL GLU GLU ALA VAL SEQRES 14 A 215 TYR ARG ALA LEU LYS LEU LYS THR LYS LEU GLY VAL SER SEQRES 15 A 215 LEU GLU GLN ALA LEU LEU ILE LEU GLU VAL ALA ALA LYS SEQRES 16 A 215 LEU GLY THR THR VAL GLU GLU ALA VAL LYS ARG ALA LEU SEQRES 17 A 215 LYS LEU LYS THR LYS LEU GLY FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 SER A 25 GLY A 40 1 16 HELIX 2 AA2 THR A 42 GLY A 58 1 17 HELIX 3 AA3 SER A 60 GLY A 75 1 16 HELIX 4 AA4 THR A 77 GLY A 93 1 17 HELIX 5 AA5 SER A 95 LEU A 109 1 15 HELIX 6 AA6 THR A 112 GLY A 128 1 17 HELIX 7 AA7 SER A 130 GLY A 145 1 16 HELIX 8 AA8 THR A 147 GLY A 163 1 17 HELIX 9 AA9 SER A 165 GLY A 180 1 16 HELIX 10 AB1 THR A 182 GLY A 198 1 17 HELIX 11 AB2 SER A 200 GLY A 215 1 16 HELIX 12 AB3 THR A 217 LYS A 231 1 15 CRYST1 36.134 60.330 54.083 90.00 93.19 90.00 P 1 21 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 0.027675 0.000000 0.001542 0.00000 SCALE2 0.000000 0.016576 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018519 0.00000 MASTER 267 0 0 12 0 0 0 6 1605 1 0 17 END