HEADER DE NOVO PROTEIN 03-AUG-16 5L33 TITLE CRYSTAL STRUCTURE OF A DE NOVO DESIGNED PROTEIN WITH CURVED BETA-SHEET COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENOVO NTF2; 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 DE NOVO NTF2, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.OBERDORFER,E.MARCOS,B.BASANTA,T.M.CHIDYAUSIKU,B.SANKARAN,D.BAKER REVDAT 3 06-MAR-24 5L33 1 REMARK REVDAT 2 01-FEB-17 5L33 1 JRNL REVDAT 1 25-JAN-17 5L33 0 JRNL AUTH E.MARCOS,B.BASANTA,T.M.CHIDYAUSIKU,Y.TANG,G.OBERDORFER, JRNL AUTH 2 G.LIU,G.V.SWAPNA,R.GUAN,D.A.SILVA,J.DOU,J.H.PEREIRA,R.XIAO, JRNL AUTH 3 B.SANKARAN,P.H.ZWART,G.T.MONTELIONE,D.BAKER JRNL TITL PRINCIPLES FOR DESIGNING PROTEINS WITH CAVITIES FORMED BY JRNL TITL 2 CURVED BETA SHEETS. JRNL REF SCIENCE V. 355 201 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28082595 JRNL DOI 10.1126/SCIENCE.AAH7389 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1616 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 6503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 307 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 50.2108 - 2.5199 0.94 3276 151 0.1653 0.1851 REMARK 3 2 2.5199 - 2.0001 0.90 2920 156 0.1922 0.2433 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 21.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 937 REMARK 3 ANGLE : 0.875 1265 REMARK 3 CHIRALITY : 0.037 130 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 17.211 371 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5915 11.5904 63.3732 REMARK 3 T TENSOR REMARK 3 T11: 0.0995 T22: 0.2882 REMARK 3 T33: 0.1931 T12: 0.0367 REMARK 3 T13: 0.0425 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.0106 L22: 0.3384 REMARK 3 L33: 0.7953 L12: 0.0029 REMARK 3 L13: 0.2237 L23: 0.4597 REMARK 3 S TENSOR REMARK 3 S11: -0.0278 S12: -0.3008 S13: -0.1340 REMARK 3 S21: -0.1052 S22: -0.0288 S23: -0.2702 REMARK 3 S31: 0.0384 S32: 0.8099 S33: 0.0152 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 36 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7903 15.2078 70.2200 REMARK 3 T TENSOR REMARK 3 T11: 0.0006 T22: 0.2225 REMARK 3 T33: 0.2138 T12: -0.0064 REMARK 3 T13: -0.0341 T23: -0.0912 REMARK 3 L TENSOR REMARK 3 L11: 0.1192 L22: 0.3572 REMARK 3 L33: 0.2302 L12: -0.0803 REMARK 3 L13: -0.1435 L23: -0.2097 REMARK 3 S TENSOR REMARK 3 S11: 0.4481 S12: 0.0666 S13: -0.1464 REMARK 3 S21: 0.7042 S22: 0.0209 S23: 0.3380 REMARK 3 S31: -0.7604 S32: -0.0328 S33: 0.0433 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 37 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3445 7.8822 64.1183 REMARK 3 T TENSOR REMARK 3 T11: 0.1947 T22: 0.1421 REMARK 3 T33: 0.1259 T12: 0.0295 REMARK 3 T13: 0.0347 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.7606 L22: 0.6434 REMARK 3 L33: 0.7246 L12: 0.4802 REMARK 3 L13: 0.3939 L23: 0.9782 REMARK 3 S TENSOR REMARK 3 S11: 0.1883 S12: -0.2082 S13: 0.0173 REMARK 3 S21: 0.1240 S22: -0.1681 S23: -0.0607 REMARK 3 S31: 0.2345 S32: -0.0010 S33: 0.0196 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8876 13.7542 59.3635 REMARK 3 T TENSOR REMARK 3 T11: 0.1669 T22: 0.1174 REMARK 3 T33: 0.1550 T12: 0.0231 REMARK 3 T13: 0.0127 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.3388 L22: 0.2891 REMARK 3 L33: 1.2752 L12: 0.1611 REMARK 3 L13: -0.0725 L23: -0.6991 REMARK 3 S TENSOR REMARK 3 S11: 0.1410 S12: -0.1006 S13: 0.0162 REMARK 3 S21: -0.1355 S22: -0.1534 S23: 0.0080 REMARK 3 S31: -0.2327 S32: -0.2210 S33: -0.0032 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 5L33 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-16 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 : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.1.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6503 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.195 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 2.5.6 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM MOPS/HEPES, PH 7.5, 12.5% REMARK 280 PEG 1000, 12.5% PEG 3350 AND 12.5% 2-METHYL-2,4-PENTANEDIOL AND REMARK 280 0.2 M OF AMINO ACIDS (SODIUM GLUTAMATE, DL-ALANINE, GLYCINE, DL- REMARK 280 LYSINE HCL AND DL-SERINE), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 14.12500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.12500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.18000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 -3 REMARK 465 SER A -2 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 206 O HOH A 232 2.11 REMARK 500 OE2 GLU A 15 O HOH A 201 2.12 REMARK 500 OE1 GLU A 15 O HOH A 202 2.17 REMARK 500 OD2 ASP A 29 O HOH A 203 2.18 REMARK 500 NH2 ARG A 31 O HOH A 204 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 5L33 A -3 104 PDB 5L33 5L33 -3 104 SEQRES 1 A 108 GLY SER HIS MET PRO GLU GLU GLU LYS ALA ALA ARG LEU SEQRES 2 A 108 PHE ILE GLU ALA LEU GLU LYS GLY ASP PRO GLU LEU MET SEQRES 3 A 108 ARG LYS VAL ILE SER PRO ASP THR ARG MET GLU ASP ASN SEQRES 4 A 108 GLY ARG GLU PHE THR GLY ASP GLU VAL VAL GLU TYR VAL SEQRES 5 A 108 LYS GLU ILE GLN LYS ARG GLY GLU GLN TRP HIS LEU ARG SEQRES 6 A 108 ARG TYR THR LYS GLU GLY ASN SER TRP ARG PHE GLU VAL SEQRES 7 A 108 GLN VAL ASP ASN ASN GLY GLN THR GLU GLN TRP GLU VAL SEQRES 8 A 108 GLN ILE GLU VAL ARG ASN GLY ARG ILE LYS ARG VAL THR SEQRES 9 A 108 ILE THR HIS VAL FORMUL 2 HOH *69(H2 O) HELIX 1 AA1 PRO A 1 GLY A 17 1 17 HELIX 2 AA2 ASP A 18 ILE A 26 1 9 HELIX 3 AA3 GLY A 41 GLY A 55 1 15 SHEET 1 AA1 6 ARG A 37 THR A 40 0 SHEET 2 AA1 6 ARG A 31 ASP A 34 -1 N MET A 32 O PHE A 39 SHEET 3 AA1 6 ARG A 95 THR A 102 1 O ILE A 101 N GLU A 33 SHEET 4 AA1 6 GLN A 81 ARG A 92 -1 N GLN A 88 O THR A 100 SHEET 5 AA1 6 SER A 69 ASN A 78 -1 N PHE A 72 O VAL A 87 SHEET 6 AA1 6 GLN A 57 GLU A 66 -1 N GLN A 57 O ASP A 77 CRYST1 28.250 34.360 100.390 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 0.035398 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009961 0.00000