HEADER DE NOVO PROTEIN 29-MAR-16 5J2L TITLE DE NOVO DESIGN OF PROTEIN HOMO-OLIGOMERS WITH MODULAR HYDROGEN BOND TITLE 2 NETWORK-MEDIATED SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DESIGN 2L4HC2_11; COMPND 3 CHAIN: B, 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; 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 3 06-MAR-24 5J2L 1 REMARK REVDAT 2 01-NOV-17 5J2L 1 REMARK REVDAT 1 25-MAY-16 5J2L 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 11049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1105 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 35.0885 - 3.9187 0.98 1265 142 0.2114 0.2233 REMARK 3 2 3.9187 - 3.1110 1.00 1257 139 0.1901 0.2146 REMARK 3 3 3.1110 - 2.7179 1.00 1245 137 0.2163 0.2705 REMARK 3 4 2.7179 - 2.4695 1.00 1256 139 0.2032 0.2699 REMARK 3 5 2.4695 - 2.2925 1.00 1229 137 0.1943 0.2609 REMARK 3 6 2.2925 - 2.1574 0.99 1237 139 0.1986 0.2452 REMARK 3 7 2.1574 - 2.0494 0.99 1232 136 0.2094 0.2410 REMARK 3 8 2.0494 - 1.9601 0.99 1223 136 0.2593 0.3290 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.740 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 : 0.013 1332 REMARK 3 ANGLE : 1.126 1762 REMARK 3 CHIRALITY : 0.063 196 REMARK 3 PLANARITY : 0.005 232 REMARK 3 DIHEDRAL : 12.442 592 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 5J2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-15 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 : 8.2.2 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 35.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 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 (%): 36.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5 AND 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 22.85000 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: DIMER ACCORDING TO GEL FILTRATION, SEC-MALS, AND SMALL- REMARK 300 ANGLE X-RAY SCATTERING (SAXS) 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 B -4 REMARK 465 SER B -3 REMARK 465 HIS B -2 REMARK 465 MET B -1 REMARK 465 GLY B 0 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 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 H THR B 38 O HOH B 101 1.07 REMARK 500 HE ARG B 49 O HOH B 102 1.19 REMARK 500 HH12 ARG B 26 O HOH B 106 1.49 REMARK 500 HZ3 LYS B 28 O HOH B 109 1.54 REMARK 500 OE2 GLU A 50 HH21 ARG A 53 1.58 REMARK 500 N THR B 38 O HOH B 101 1.87 REMARK 500 O HOH A 117 O HOH A 137 1.88 REMARK 500 NE ARG B 49 O HOH B 102 1.94 REMARK 500 OE1 GLN B 31 O HOH B 103 1.95 REMARK 500 OE1 GLU B 43 O HOH B 104 1.99 REMARK 500 O HOH A 106 O HOH A 134 2.01 REMARK 500 OE2 GLU A 12 O HOH A 101 2.01 REMARK 500 OE1 GLU B 57 O HOH B 105 2.04 REMARK 500 OE1 GLU B 47 O HOH B 106 2.13 REMARK 500 CB GLU B 36 O HOH B 101 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 HZ1 LYS A 28 OE2 GLU A 64 2546 1.31 REMARK 500 HA SER A 1 O HOH B 125 1455 1.59 REMARK 500 NZ LYS A 28 OE2 GLU A 64 2546 2.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 5J2L B -4 76 PDB 5J2L 5J2L -4 76 DBREF 5J2L A -4 76 PDB 5J2L 5J2L -4 76 SEQRES 1 B 81 GLY SER HIS MET GLY SER GLU ASP TYR LYS LEU ARG GLU SEQRES 2 B 81 ALA GLN ARG GLU LEU ASP LYS GLN ARG LYS ASP THR GLU SEQRES 3 B 81 GLU ILE ARG LYS ARG LEU LYS GLU ILE GLN ARG LEU THR SEQRES 4 B 81 ASP GLU ARG THR SER THR ALA ASP GLU LEU ILE LYS GLU SEQRES 5 B 81 LEU ARG GLU ILE ILE ARG ARG LEU GLN GLU GLN SER GLU SEQRES 6 B 81 LYS LEU ARG GLU ILE ILE GLU GLU LEU GLU LYS ILE ILE SEQRES 7 B 81 ARG LYS ARG SEQRES 1 A 81 GLY SER HIS MET GLY SER GLU ASP TYR LYS LEU ARG GLU SEQRES 2 A 81 ALA GLN ARG GLU LEU ASP LYS GLN ARG LYS ASP THR GLU SEQRES 3 A 81 GLU ILE ARG LYS ARG LEU LYS GLU ILE GLN ARG LEU THR SEQRES 4 A 81 ASP GLU ARG THR SER THR ALA ASP GLU LEU ILE LYS GLU SEQRES 5 A 81 LEU ARG GLU ILE ILE ARG ARG LEU GLN GLU GLN SER GLU SEQRES 6 A 81 LYS LEU ARG GLU ILE ILE GLU GLU LEU GLU LYS ILE ILE SEQRES 7 A 81 ARG LYS ARG FORMUL 3 HOH *80(H2 O) HELIX 1 AA1 SER B 1 ARG B 37 1 37 HELIX 2 AA2 THR B 40 ARG B 76 1 37 HELIX 3 AA3 GLU A 2 ARG A 37 1 36 HELIX 4 AA4 THR A 40 ARG A 76 1 37 CRYST1 35.380 45.700 48.320 90.00 97.43 90.00 P 1 21 1 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 0.028265 0.000000 0.003686 0.00000 SCALE2 0.000000 0.021882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020871 0.00000