HEADER DE NOVO PROTEIN 25-MAR-14 4P6L TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED TRANSMEMBRANE TITLE 2 METALLOTRANSPORTER IN OCTYL GLUCOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPUTATIONALLY DESIGNED TRANSPORTER OF ZN(II) AND PROTON; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS TRANSMEMBRANE, TRANSPORTER, DE-NOVO DESIGNED, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.H.JOH,R.ACHARYA,W.F.DEGRADO REVDAT 8 30-OCT-24 4P6L 1 REMARK REVDAT 7 27-DEC-23 4P6L 1 REMARK REVDAT 6 11-DEC-19 4P6L 1 REMARK REVDAT 5 01-NOV-17 4P6L 1 REMARK REVDAT 4 20-SEP-17 4P6L 1 SOURCE JRNL REMARK REVDAT 3 14-JAN-15 4P6L 1 DBREF REVDAT 2 31-DEC-14 4P6L 1 JRNL REVDAT 1 24-DEC-14 4P6L 0 JRNL AUTH N.H.JOH,T.WANG,M.P.BHATE,R.ACHARYA,Y.WU,M.GRABE,M.HONG, JRNL AUTH 2 G.GRIGORYAN,W.F.DEGRADO JRNL TITL DE NOVO DESIGN OF A TRANSMEMBRANE ZN2+-TRANSPORTING JRNL TITL 2 FOUR-HELIX BUNDLE. JRNL REF SCIENCE V. 346 1520 2014 JRNL REFN ESSN 1095-9203 JRNL PMID 25525248 JRNL DOI 10.1126/SCIENCE.1261172 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 2598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.294 REMARK 3 R VALUE (WORKING SET) : 0.292 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 261 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 43.5652 - 3.5313 0.94 1206 138 0.2781 0.2826 REMARK 3 2 3.5313 - 2.8030 0.90 1131 123 0.3622 0.4069 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.010 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 : 0.002 434 REMARK 3 ANGLE : 0.399 588 REMARK 3 CHIRALITY : 0.017 64 REMARK 3 PLANARITY : 0.001 70 REMARK 3 DIHEDRAL : 10.225 144 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 4P6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115869 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2699 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 61.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 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 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1:1 (VOL.) MIXTURE OF OG-BOUND ROCKER REMARK 280 (1 MM PEPTIDE, 1 MM COSO4, 50 MM OG) AND THE WELL SOLUTION (360 REMARK 280 MM LICL, 100 MM SODIUM CITRATE (PH 5.6), 28 % (W/V) PEG 400, REMARK 280 1.56M 1,2-HEXANEDEDIOL) INVERTED ABOVE THE WELL SOLUTION AND REMARK 280 INCUBATED AT ROOM TEMPERATURE OVER 2.5 WEEKS, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 43.56000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 43.56000 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 43.56000 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 43.56000 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 43.56000 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 43.56000 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 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: THE BIOLOGICAL UNIT WAS DETERMINED BY COMBINED APPROACH OF REMARK 300 COMPUTATIONAL DESIGN, ANALYTICAL ULTRACENTRIFUGATION AND 19F-CODEX REMARK 300 VIA SOLID-STATE NMR. AS PER THE AUTHORS THIS TETRAMERIC ASSEMBLY IS REMARK 300 REPORTED IN THE SEPARATE ENTRY (PDB ID: 2MUZ) FOR THE SOLID-STATE REMARK 300 NMR MODEL ACCOMPANIED BY THE PAPER THAT CITES THIS PDB 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P6J RELATED DB: PDB REMARK 900 RELATED ID: 4P6K RELATED DB: PDB DBREF 4P6L A 1 26 PDB 4P6L 4P6L 1 26 DBREF 4P6L B 1 26 PDB 4P6L 4P6L 1 26 SEQRES 1 A 26 TYR TYR LYS GLU ILE ALA HIS ALA LEU PHE SER ALA LEU SEQRES 2 A 26 PHE ALA LEU SER GLU LEU TYR ILE ALA VAL ARG TYR NH2 SEQRES 1 B 26 TYR TYR LYS GLU ILE ALA HIS ALA LEU PHE SER ALA LEU SEQRES 2 B 26 PHE ALA LEU SER GLU LEU TYR ILE ALA VAL ARG TYR NH2 HET NH2 A 26 1 HET NH2 B 26 1 HETNAM NH2 AMINO GROUP FORMUL 1 NH2 2(H2 N) HELIX 1 AA1 TYR A 1 TYR A 25 1 25 HELIX 2 AA2 TYR B 2 TYR B 25 1 24 LINK C TYR A 25 N NH2 A 26 1555 1555 1.33 LINK C TYR B 25 N NH2 B 26 1555 1555 1.33 CRYST1 87.120 87.120 87.120 90.00 90.00 90.00 I 21 3 48 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 0.011478 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011478 0.00000