HEADER DE NOVO PROTEIN 17-JUN-14 3WWB TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED PIZZA2-SR PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIZZA2-SR PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS DESIGNED. KEYWDS COMPUTATIONAL PROTEIN DESIGN, SELF-ASSEMBLY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.D.VOET,H.NOGUCHI,C.ADDY,D.SIMONCINI,D.TERADA,S.UNZAI,S.Y.PARK, AUTHOR 2 K.Y.J.ZHANG,J.R.H.TAME REVDAT 3 20-MAR-24 3WWB 1 REMARK REVDAT 2 05-NOV-14 3WWB 1 JRNL REVDAT 1 08-OCT-14 3WWB 0 JRNL AUTH A.R.D.VOET,H.NOGUCHI,C.ADDY,D.SIMONCINI,D.TERADA,S.UNZAI, JRNL AUTH 2 S.Y.PARK,K.Y.J.ZHANG,J.R.H.TAME JRNL TITL COMPUTATIONAL DESIGN OF A SELF-ASSEMBLING SYMMETRICAL JRNL TITL 2 BETA-PROPELLER PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 15102 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 25288768 JRNL DOI 10.1073/PNAS.1412768111 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1412) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 30629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1544 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 34.9589 - 3.7797 0.94 2671 151 0.1578 0.1845 REMARK 3 2 3.7797 - 3.0006 1.00 2705 130 0.1625 0.1920 REMARK 3 3 3.0006 - 2.6215 1.00 2685 135 0.1791 0.2114 REMARK 3 4 2.6215 - 2.3818 1.00 2652 143 0.1867 0.2033 REMARK 3 5 2.3818 - 2.2112 1.00 2640 137 0.1649 0.2031 REMARK 3 6 2.2112 - 2.0808 1.00 2679 125 0.1724 0.2080 REMARK 3 7 2.0808 - 1.9766 1.00 2620 141 0.1618 0.2187 REMARK 3 8 1.9766 - 1.8906 1.00 2625 139 0.1659 0.1871 REMARK 3 9 1.8906 - 1.8178 1.00 2609 144 0.1806 0.2219 REMARK 3 10 1.8178 - 1.7551 1.00 2603 154 0.1997 0.2378 REMARK 3 11 1.7551 - 1.7002 0.99 2596 145 0.2027 0.2432 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 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 1790 REMARK 3 ANGLE : 1.180 2459 REMARK 3 CHIRALITY : 0.076 318 REMARK 3 PLANARITY : 0.005 323 REMARK 3 DIHEDRAL : 8.833 617 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 3WWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000096873. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.280 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 (%): 50.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M LITHIUM CHLORIDE, 0.1M TRIS-HCL PH REMARK 280 8.0, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 30.72450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.95150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.84750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.95150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.72450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.84750 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 ARG A 0 REMARK 465 SER A 1 REMARK 465 GLY A 84 REMARK 465 SER A 85 REMARK 465 GLY B -4 REMARK 465 SER B -3 REMARK 465 HIS B -2 REMARK 465 MET B -1 REMARK 465 ARG B 0 REMARK 465 GLY B 84 REMARK 465 SER B 85 REMARK 465 GLY C -4 REMARK 465 SER C -3 REMARK 465 HIS C -2 REMARK 465 MET C -1 REMARK 465 ARG C 0 REMARK 465 SER C 1 REMARK 465 GLY C 84 REMARK 465 SER C 85 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 PRO A 8 42.45 -82.93 REMARK 500 PRO A 50 48.08 -80.68 REMARK 500 PRO C 8 46.13 -76.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WW7 RELATED DB: PDB REMARK 900 RELATED ID: 3WW8 RELATED DB: PDB REMARK 900 RELATED ID: 3WW9 RELATED DB: PDB REMARK 900 RELATED ID: 3WWA RELATED DB: PDB REMARK 900 RELATED ID: 3WWF RELATED DB: PDB DBREF 3WWB A -4 85 PDB 3WWB 3WWB -4 85 DBREF 3WWB B -4 85 PDB 3WWB 3WWB -4 85 DBREF 3WWB C -4 85 PDB 3WWB 3WWB -4 85 SEQRES 1 A 90 GLY SER HIS MET ARG SER ASN THR GLN THR VAL LEU PRO SEQRES 2 A 90 PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SEQRES 3 A 90 SER ALA GLY THR VAL TYR VAL THR ASP ARG GLY ASN ASN SEQRES 4 A 90 ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR SEQRES 5 A 90 VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL SEQRES 6 A 90 ALA VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP ARG SEQRES 7 A 90 GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER SEQRES 1 B 90 GLY SER HIS MET ARG SER ASN THR GLN THR VAL LEU PRO SEQRES 2 B 90 PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SEQRES 3 B 90 SER ALA GLY THR VAL TYR VAL THR ASP ARG GLY ASN ASN SEQRES 4 B 90 ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR SEQRES 5 B 90 VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL SEQRES 6 B 90 ALA VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP ARG SEQRES 7 B 90 GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER SEQRES 1 C 90 GLY SER HIS MET ARG SER ASN THR GLN THR VAL LEU PRO SEQRES 2 C 90 PHE THR GLY LEU ASN THR PRO SER GLY VAL ALA VAL ASP SEQRES 3 C 90 SER ALA GLY THR VAL TYR VAL THR ASP ARG GLY ASN ASN SEQRES 4 C 90 ARG VAL VAL LYS LEU ALA ALA GLY SER ASN THR GLN THR SEQRES 5 C 90 VAL LEU PRO PHE THR GLY LEU ASN THR PRO SER GLY VAL SEQRES 6 C 90 ALA VAL ASP SER ALA GLY THR VAL TYR VAL THR ASP ARG SEQRES 7 C 90 GLY ASN ASN ARG VAL VAL LYS LEU ALA ALA GLY SER FORMUL 4 HOH *239(H2 O) HELIX 1 1 ARG A 31 ASN A 34 5 4 HELIX 2 2 ARG A 73 ASN A 76 5 4 HELIX 3 3 ARG B 31 ASN B 34 5 4 HELIX 4 4 ARG B 73 ASN B 76 5 4 HELIX 5 5 ARG C 31 ASN C 34 5 4 HELIX 6 6 ARG C 73 ASN C 76 5 4 SHEET 1 A 4 THR A 5 VAL A 6 0 SHEET 2 A 4 ARG C 77 LEU C 81 -1 O LYS C 80 N THR A 5 SHEET 3 A 4 VAL C 68 ASP C 72 -1 N VAL C 70 O VAL C 79 SHEET 4 A 4 ALA C 61 VAL C 62 -1 N ALA C 61 O TYR C 69 SHEET 1 B 4 ALA A 19 VAL A 20 0 SHEET 2 B 4 VAL A 26 ASP A 30 -1 O TYR A 27 N ALA A 19 SHEET 3 B 4 ARG A 35 LEU A 39 -1 O VAL A 37 N VAL A 28 SHEET 4 B 4 GLN A 46 VAL A 48 -1 O THR A 47 N LYS A 38 SHEET 1 C 4 ALA A 61 VAL A 62 0 SHEET 2 C 4 VAL A 68 ASP A 72 -1 O TYR A 69 N ALA A 61 SHEET 3 C 4 ARG A 77 LEU A 81 -1 O VAL A 79 N VAL A 70 SHEET 4 C 4 GLN B 4 VAL B 6 -1 O THR B 5 N LYS A 80 SHEET 1 D 4 ALA B 19 VAL B 20 0 SHEET 2 D 4 VAL B 26 ASP B 30 -1 O TYR B 27 N ALA B 19 SHEET 3 D 4 ARG B 35 LEU B 39 -1 O VAL B 37 N VAL B 28 SHEET 4 D 4 THR B 47 VAL B 48 -1 O THR B 47 N LYS B 38 SHEET 1 E 4 ALA B 61 VAL B 62 0 SHEET 2 E 4 VAL B 68 ASP B 72 -1 O TYR B 69 N ALA B 61 SHEET 3 E 4 ARG B 77 LEU B 81 -1 O ARG B 77 N ASP B 72 SHEET 4 E 4 THR C 5 VAL C 6 -1 O THR C 5 N LYS B 80 SHEET 1 F 4 ALA C 19 VAL C 20 0 SHEET 2 F 4 VAL C 26 ASP C 30 -1 O TYR C 27 N ALA C 19 SHEET 3 F 4 ARG C 35 LEU C 39 -1 O VAL C 37 N VAL C 28 SHEET 4 F 4 THR C 47 VAL C 48 -1 O THR C 47 N LYS C 38 CRYST1 61.449 63.695 69.903 90.00 90.00 90.00 P 21 21 21 12 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 0.016274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014306 0.00000