HEADER DE NOVO PROTEIN 28-MAR-16 5J0J TITLE DE NOVO DESIGN OF PROTEIN HOMO-OLIGOMERS WITH MODULAR HYDROGEN BOND TITLE 2 NETWORK-MEDIATED SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED PROTEIN 2L6HC3_6; COMPND 3 CHAIN: A, B, C; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSETTA, DE NOVO DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.SANKARAN,P.H.ZWART,J.H.PEREIRA,D.BAKER,S.BOYKEN,Z.CHEN,B.GROVES, AUTHOR 2 R.A.LANGAN,G.OBERDORFER,A.FORD,J.GILMORE,C.XU,F.DIMAIO,G.SEELIG REVDAT 2 06-MAR-24 5J0J 1 REMARK REVDAT 1 25-MAY-16 5J0J 0 JRNL AUTH S.E.BOYKEN,Z.CHEN,B.GROVES,R.A.LANGAN,G.OBERDORFER,A.FORD, JRNL AUTH 2 J.M.GILMORE,C.XU,F.DIMAIO,J.H.PEREIRA,B.SANKARAN,G.SEELIG, JRNL AUTH 3 P.H.ZWART,D.BAKER JRNL TITL DE NOVO DESIGN OF PROTEIN HOMO-OLIGOMERS WITH MODULAR JRNL TITL 2 HYDROGEN-BOND NETWORK-MEDIATED SPECIFICITY. JRNL REF SCIENCE V. 352 680 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27151862 JRNL DOI 10.1126/SCIENCE.AAD8865 REMARK 2 REMARK 2 RESOLUTION. 2.26 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 9727 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 970 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 49.9784 - 4.3145 0.94 1267 140 0.2422 0.2963 REMARK 3 2 4.3145 - 3.4248 1.00 1305 147 0.1907 0.2460 REMARK 3 3 3.4248 - 2.9920 1.00 1315 141 0.2298 0.2796 REMARK 3 4 2.9920 - 2.7184 1.00 1278 138 0.2342 0.2771 REMARK 3 5 2.7184 - 2.5236 1.00 1286 145 0.2463 0.2452 REMARK 3 6 2.5236 - 2.3748 0.99 1284 139 0.2344 0.3049 REMARK 3 7 2.3748 - 2.2559 0.82 1022 120 0.2738 0.3243 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 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 : 0.008 1732 REMARK 3 ANGLE : 0.799 2309 REMARK 3 CHIRALITY : 0.039 280 REMARK 3 PLANARITY : 0.003 291 REMARK 3 DIHEDRAL : 18.505 729 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 5J0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-14 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 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9728 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.256 REMARK 200 RESOLUTION RANGE LOW (A) : 49.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE, 0.1 M MES PH REMARK 280 5.5 , 20 % PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 17.19300 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 300 REMARK: TRIMER ACCORDING TO 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 THR A 1 REMARK 465 GLU A 72 REMARK 465 SER A 73 REMARK 465 ASP A 74 REMARK 465 GLY B -4 REMARK 465 SER B -3 REMARK 465 HIS B -2 REMARK 465 MET B -1 REMARK 465 GLY B 0 REMARK 465 THR B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 72 REMARK 465 SER B 73 REMARK 465 ASP B 74 REMARK 465 GLY C -4 REMARK 465 SER C -3 REMARK 465 HIS C -2 REMARK 465 MET C -1 REMARK 465 GLY C 0 REMARK 465 GLU C 72 REMARK 465 SER C 73 REMARK 465 ASP C 74 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 C 104 O HOH C 119 2.16 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 31 34.28 -96.08 REMARK 500 PRO A 37 63.85 -67.88 REMARK 500 ASP A 40 -16.20 66.83 REMARK 500 LYS B 4 -80.94 73.38 REMARK 500 LYS B 35 -70.91 -84.32 REMARK 500 ASP B 38 -147.91 -130.05 REMARK 500 ASN C 36 92.03 -170.79 REMARK 500 ASP C 38 -175.92 -68.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 5J0J A -4 74 PDB 5J0J 5J0J -4 74 DBREF 5J0J B -4 74 PDB 5J0J 5J0J -4 74 DBREF 5J0J C -4 74 PDB 5J0J 5J0J -4 74 SEQRES 1 A 79 GLY SER HIS MET GLY THR LYS TYR LYS ILE LYS GLU THR SEQRES 2 A 79 LEU LYS ARG LEU GLU ASP SER LEU ARG GLU LEU ARG ARG SEQRES 3 A 79 ILE LEU GLU GLU LEU LYS GLU MET LEU GLU ARG LEU GLU SEQRES 4 A 79 LYS ASN PRO ASP LYS ASP VAL ILE VAL GLU VAL LEU LYS SEQRES 5 A 79 VAL ILE VAL LYS ALA ILE GLU ALA SER VAL GLU ASN GLN SEQRES 6 A 79 ARG ILE SER ALA GLU ASN GLN LYS ALA LEU ALA GLU SER SEQRES 7 A 79 ASP SEQRES 1 B 79 GLY SER HIS MET GLY THR LYS TYR LYS ILE LYS GLU THR SEQRES 2 B 79 LEU LYS ARG LEU GLU ASP SER LEU ARG GLU LEU ARG ARG SEQRES 3 B 79 ILE LEU GLU GLU LEU LYS GLU MET LEU GLU ARG LEU GLU SEQRES 4 B 79 LYS ASN PRO ASP LYS ASP VAL ILE VAL GLU VAL LEU LYS SEQRES 5 B 79 VAL ILE VAL LYS ALA ILE GLU ALA SER VAL GLU ASN GLN SEQRES 6 B 79 ARG ILE SER ALA GLU ASN GLN LYS ALA LEU ALA GLU SER SEQRES 7 B 79 ASP SEQRES 1 C 79 GLY SER HIS MET GLY THR LYS TYR LYS ILE LYS GLU THR SEQRES 2 C 79 LEU LYS ARG LEU GLU ASP SER LEU ARG GLU LEU ARG ARG SEQRES 3 C 79 ILE LEU GLU GLU LEU LYS GLU MET LEU GLU ARG LEU GLU SEQRES 4 C 79 LYS ASN PRO ASP LYS ASP VAL ILE VAL GLU VAL LEU LYS SEQRES 5 C 79 VAL ILE VAL LYS ALA ILE GLU ALA SER VAL GLU ASN GLN SEQRES 6 C 79 ARG ILE SER ALA GLU ASN GLN LYS ALA LEU ALA GLU SER SEQRES 7 C 79 ASP FORMUL 4 HOH *39(H2 O) HELIX 1 AA1 LYS A 2 GLU A 31 1 30 HELIX 2 AA2 ASP A 40 ALA A 71 1 32 HELIX 3 AA3 LYS B 4 ASN B 36 1 33 HELIX 4 AA4 LYS B 39 ALA B 71 1 33 HELIX 5 AA5 LYS C 2 ASN C 36 1 35 HELIX 6 AA6 LYS C 39 ALA C 71 1 33 CRYST1 50.010 34.386 61.542 90.00 92.40 90.00 P 1 21 1 6 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 0.019996 0.000000 0.000837 0.00000 SCALE2 0.000000 0.029082 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016263 0.00000