HEADER DE NOVO PROTEIN 05-APR-16 5J73 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_9; COMPND 3 CHAIN: A, B, C, D; 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 5J73 1 REMARK REVDAT 2 01-NOV-17 5J73 1 REMARK REVDAT 1 25-MAY-16 5J73 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. 2.56 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 944 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 38.7748 - 4.8948 0.99 1225 138 0.1790 0.2088 REMARK 3 2 4.8948 - 3.8863 1.00 1227 131 0.1794 0.2303 REMARK 3 3 3.8863 - 3.3954 1.00 1205 133 0.2039 0.2527 REMARK 3 4 3.3954 - 3.0851 1.00 1215 141 0.2340 0.2884 REMARK 3 5 3.0851 - 2.8640 1.00 1199 131 0.2584 0.3380 REMARK 3 6 2.8640 - 2.6952 1.00 1201 141 0.2495 0.2716 REMARK 3 7 2.6952 - 2.5602 1.00 1233 129 0.2830 0.3704 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.990 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 : 0.005 2471 REMARK 3 ANGLE : 0.838 3290 REMARK 3 CHIRALITY : 0.033 380 REMARK 3 PLANARITY : 0.003 435 REMARK 3 DIHEDRAL : 16.151 1042 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 5J73 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219930. 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 : 9454 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 38.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DEHYDRATE PH 5.0, 30 % PEG MME 550, VAPOR DIFFUSION, SITTING REMARK 280 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 45.98500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 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: 3010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 SER A 76 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 SER B 76 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 GLN C 75 REMARK 465 SER C 76 REMARK 465 GLY D -4 REMARK 465 SER D -3 REMARK 465 HIS D -2 REMARK 465 MET D -1 REMARK 465 GLY D 0 REMARK 465 THR D 1 REMARK 465 GLN D 75 REMARK 465 SER D 76 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 HH22 ARG B 59 O HOH B 101 1.10 REMARK 500 OE2 GLU A 55 HH12 ARG D 59 1.54 REMARK 500 NH2 ARG B 59 O HOH B 101 1.87 REMARK 500 NH2 ARG A 62 OE2 GLU B 24 2.05 REMARK 500 OD1 ASP B 45 NH2 ARG B 48 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 NZ LYS A 73 OD2 ASP B 41 2545 2.11 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 LYS A 35 35.38 -92.65 REMARK 500 ASN A 74 59.76 -92.32 REMARK 500 SER B 40 -51.09 -18.07 REMARK 500 SER C 2 107.09 112.83 REMARK 500 LYS C 35 31.60 -90.92 REMARK 500 SER C 39 173.15 -50.38 REMARK 500 VAL D 38 -126.10 -85.69 REMARK 500 SER D 40 -50.60 69.69 REMARK 500 LYS D 73 -85.04 -81.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 5J73 A -4 76 PDB 5J73 5J73 -4 76 DBREF 5J73 B -4 76 PDB 5J73 5J73 -4 76 DBREF 5J73 C -4 76 PDB 5J73 5J73 -4 76 DBREF 5J73 D -4 76 PDB 5J73 5J73 -4 76 SEQRES 1 A 81 GLY SER HIS MET GLY THR SER ASP TYR ILE ILE GLU GLN SEQRES 2 A 81 ILE GLN ARG ASP GLN GLU GLU ALA ARG LYS LYS VAL GLU SEQRES 3 A 81 GLU ALA GLU GLU ARG LEU GLU ARG VAL LYS GLU ALA SER SEQRES 4 A 81 LYS ARG GLY VAL SER SER ASP GLN LEU LEU ASP LEU ILE SEQRES 5 A 81 ARG GLU LEU ALA GLU ILE ILE GLU GLU LEU ILE ARG ILE SEQRES 6 A 81 ILE ARG ARG SER ASN GLU ALA ILE LYS GLU LEU ILE LYS SEQRES 7 A 81 ASN GLN SER SEQRES 1 B 81 GLY SER HIS MET GLY THR SER ASP TYR ILE ILE GLU GLN SEQRES 2 B 81 ILE GLN ARG ASP GLN GLU GLU ALA ARG LYS LYS VAL GLU SEQRES 3 B 81 GLU ALA GLU GLU ARG LEU GLU ARG VAL LYS GLU ALA SER SEQRES 4 B 81 LYS ARG GLY VAL SER SER ASP GLN LEU LEU ASP LEU ILE SEQRES 5 B 81 ARG GLU LEU ALA GLU ILE ILE GLU GLU LEU ILE ARG ILE SEQRES 6 B 81 ILE ARG ARG SER ASN GLU ALA ILE LYS GLU LEU ILE LYS SEQRES 7 B 81 ASN GLN SER SEQRES 1 C 81 GLY SER HIS MET GLY THR SER ASP TYR ILE ILE GLU GLN SEQRES 2 C 81 ILE GLN ARG ASP GLN GLU GLU ALA ARG LYS LYS VAL GLU SEQRES 3 C 81 GLU ALA GLU GLU ARG LEU GLU ARG VAL LYS GLU ALA SER SEQRES 4 C 81 LYS ARG GLY VAL SER SER ASP GLN LEU LEU ASP LEU ILE SEQRES 5 C 81 ARG GLU LEU ALA GLU ILE ILE GLU GLU LEU ILE ARG ILE SEQRES 6 C 81 ILE ARG ARG SER ASN GLU ALA ILE LYS GLU LEU ILE LYS SEQRES 7 C 81 ASN GLN SER SEQRES 1 D 81 GLY SER HIS MET GLY THR SER ASP TYR ILE ILE GLU GLN SEQRES 2 D 81 ILE GLN ARG ASP GLN GLU GLU ALA ARG LYS LYS VAL GLU SEQRES 3 D 81 GLU ALA GLU GLU ARG LEU GLU ARG VAL LYS GLU ALA SER SEQRES 4 D 81 LYS ARG GLY VAL SER SER ASP GLN LEU LEU ASP LEU ILE SEQRES 5 D 81 ARG GLU LEU ALA GLU ILE ILE GLU GLU LEU ILE ARG ILE SEQRES 6 D 81 ILE ARG ARG SER ASN GLU ALA ILE LYS GLU LEU ILE LYS SEQRES 7 D 81 ASN GLN SER FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 SER A 2 LYS A 35 1 34 HELIX 2 AA2 SER A 39 ASN A 74 1 36 HELIX 3 AA3 SER B 2 LYS B 35 1 34 HELIX 4 AA4 SER B 39 ASN B 74 1 36 HELIX 5 AA5 SER C 2 LYS C 35 1 34 HELIX 6 AA6 SER C 39 LYS C 73 1 35 HELIX 7 AA7 ASP D 3 ARG D 36 1 34 HELIX 8 AA8 SER D 40 ASN D 74 1 35 CRYST1 37.790 91.970 45.840 90.00 111.14 90.00 P 1 21 1 8 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 0.026462 0.000000 0.010232 0.00000 SCALE2 0.000000 0.010873 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023389 0.00000