HEADER DE NOVO PROTEIN 28-JUL-15 5CW9 TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED FERREDOXIN-FERREDOXIN DOMAIN TITLE 2 INSERTION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED FERREDOXIN-FERREDOXIN DOMAIN INSERTION COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DESIGNED, DE NOVO, FERREDOXIN, DOMAIN INSERTION, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.DIMAIO,I.C.KING,J.GLEIXNER,L.DOYLE,B.STODDARD,D.BAKER REVDAT 5 06-MAR-24 5CW9 1 REMARK REVDAT 4 01-JAN-20 5CW9 1 REMARK REVDAT 3 01-NOV-17 5CW9 1 REMARK REVDAT 2 23-DEC-15 5CW9 1 JRNL REVDAT 1 23-SEP-15 5CW9 0 JRNL AUTH I.C.KING,J.GLEIXNER,L.DOYLE,A.KUZIN,J.F.HUNT,R.XIAO, JRNL AUTH 2 G.T.MONTELIONE,B.L.STODDARD,F.DIMAIO,D.BAKER JRNL TITL PRECISE ASSEMBLY OF COMPLEX BETA SHEET TOPOLOGIES FROM DE JRNL TITL 2 NOVO DESIGNED BUILDING BLOCKS. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26650357 JRNL DOI 10.7554/ELIFE.11012 REMARK 2 REMARK 2 RESOLUTION. 3.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 6783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.335 REMARK 3 R VALUE (WORKING SET) : 0.333 REMARK 3 FREE R VALUE : 0.349 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 675 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 40.2849 - 5.3118 0.98 1315 145 0.2692 0.2898 REMARK 3 2 5.3118 - 4.2176 0.99 1250 138 0.3711 0.3612 REMARK 3 3 4.2176 - 3.6849 0.99 1218 136 0.4595 0.5363 REMARK 3 4 3.6849 - 3.3481 0.98 1204 132 0.4604 0.4889 REMARK 3 5 3.3481 - 3.1082 0.92 1121 124 0.4583 0.4444 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 53.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 219.1 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 : 0.019 1194 REMARK 3 ANGLE : 1.711 1607 REMARK 3 CHIRALITY : 0.089 192 REMARK 3 PLANARITY : 0.007 204 REMARK 3 DIHEDRAL : 10.250 469 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 5CW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6783 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.282 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 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 (%): 77.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 3.5 M NACL, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -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 40.28150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 40.28150 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.34150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.67075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.28150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 167.01225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 167.01225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.28150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.67075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 40.28150 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 111.34150 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 40.28150 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 111.34150 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 40.28150 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 167.01225 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 55.67075 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 40.28150 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 55.67075 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 167.01225 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 40.28150 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 40.28150 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 111.34150 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 300 REMARK: MONOMER ACCORDING TO GEL FILTRATION 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 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 PRO A 12 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 PRO A 85 C - N - CA ANGL. DEV. = 11.5 DEGREES REMARK 500 PRO A 118 C - N - CA ANGL. DEV. = 10.2 DEGREES 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 GLU A 2 137.47 -170.42 REMARK 500 GLU A 13 -47.61 -17.53 REMARK 500 ALA A 30 74.36 -49.80 REMARK 500 THR A 139 98.33 -51.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KYZ RELATED DB: PDB REMARK 900 RELATED ID: 4KY3 RELATED DB: PDB DBREF 5CW9 A 1 146 PDB 5CW9 5CW9 1 146 SEQRES 1 A 146 MET GLU MET ASP ILE ARG PHE ARG GLY ASP ASP PRO GLU SEQRES 2 A 146 ALA TYR TYR LYS ALA LEU ARG GLU MET ILE ARG GLN ALA SEQRES 3 A 146 ARG LYS PHE ALA GLY THR VAL THR VAL THR LEU ILE ILE SEQRES 4 A 146 ARG PHE ARG GLY ASP ASP LEU GLU ALA LEU GLU LYS ALA SEQRES 5 A 146 LEU LYS GLU MET ILE ARG GLN ALA ARG LYS PHE ALA GLY SEQRES 6 A 146 THR VAL THR TYR THR LEU ASP GLY ASN ASP LEU GLU ILE SEQRES 7 A 146 ARG ILE THR GLY VAL PRO PRO GLN VAL ILE LEU GLU LEU SEQRES 8 A 146 VAL LYS GLU ALA ILE ARG LEU ALA LYS GLU PHE ASN ILE SEQRES 9 A 146 THR VAL THR VAL GLU LEU VAL ILE ARG ILE THR GLY VAL SEQRES 10 A 146 PRO GLU GLN VAL ARG LYS GLU LEU ALA LYS GLU ALA GLU SEQRES 11 A 146 ARG LEU ALA LYS GLU PHE ASN ILE THR VAL THR TYR THR SEQRES 12 A 146 ILE ARG LEU HELIX 1 AA1 GLU A 13 PHE A 29 1 17 HELIX 2 AA2 ASP A 45 LYS A 62 1 18 HELIX 3 AA3 PRO A 84 PHE A 102 1 19 HELIX 4 AA4 PRO A 118 ASN A 137 1 20 SHEET 1 AA1 6 THR A 66 LEU A 71 0 SHEET 2 AA1 6 ASP A 75 THR A 81 -1 O GLU A 77 N THR A 70 SHEET 3 AA1 6 THR A 32 ARG A 42 -1 N LEU A 37 O ILE A 80 SHEET 4 AA1 6 THR A 105 THR A 115 -1 O VAL A 111 N THR A 36 SHEET 5 AA1 6 GLU A 2 ARG A 8 -1 N PHE A 7 O LEU A 110 SHEET 6 AA1 6 THR A 139 ARG A 145 -1 O ARG A 145 N GLU A 2 CRYST1 80.563 80.563 222.683 90.00 90.00 90.00 I 41 2 2 16 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 0.012413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004491 0.00000