HEADER DE NOVO PROTEIN 25-MAR-14 4P6K TITLE CRYSTAL STRUCTURE OF THE COMPUTATIONALLY DESIGNED TRANSMEMBRANE TITLE 2 METALLOTRANSPORTER WITH 4-BROMOPHENYLALANINE IN LIPIDIC CUBIC PHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPUTATIONALLY DESIGNED TRANSPORTER OF ZN(II) AND PROTON; COMPND 3 CHAIN: A; 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, LIPIDIC CUBIC PHASE, DE-NOVO DESIGNED, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.H.JOH,R.ACHARYA,W.F.DEGRADO REVDAT 8 27-MAR-24 4P6K 1 REMARK REVDAT 7 27-DEC-23 4P6K 1 REMARK REVDAT 6 11-DEC-19 4P6K 1 REMARK REVDAT 5 01-NOV-17 4P6K 1 REMARK REVDAT 4 20-SEP-17 4P6K 1 SOURCE JRNL REMARK REVDAT 3 14-JAN-15 4P6K 1 DBREF REVDAT 2 31-DEC-14 4P6K 1 JRNL REVDAT 1 24-DEC-14 4P6K 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 1601 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.296 REMARK 3 R VALUE (WORKING SET) : 0.295 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 44.460 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 : 0.003 217 REMARK 3 ANGLE : 0.386 294 REMARK 3 CHIRALITY : 0.021 32 REMARK 3 PLANARITY : 0.001 35 REMARK 3 DIHEDRAL : 11.073 71 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 4P6K 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_1000200197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-12 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1601 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.0000 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: NULL REMARK 200 STARTING MODEL: 25-RESIDUE-LONG IDEALIZED HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 NL BOLUSES CONTAINING MONOOLEIN REMARK 280 -BOUND ROCKER BR-PHE2 (4 MM PEPTIDE, 60% (VOL) MONOOLEIN, 6 MM REMARK 280 ZNSO4) IMMERSED IN 1 ?L OF PRECIPITATION BUFFER (0.05 M LI2SO4, REMARK 280 0.1 M TRICINE (PH 7.4), 7 % (W/V) PEG 3000) INCUBATED IN 0.1-MM- REMARK 280 DEEP WELLS AT ROOM TEMPERATURE OVER A MONTH, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 23.43500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 23.43500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.30150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.15075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.43500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.45225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.45225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.43500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.15075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 23.43500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.30150 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 23.43500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 30.30150 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 23.43500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 45.45225 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 15.15075 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.43500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 15.15075 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 45.45225 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 23.43500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 23.43500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 30.30150 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: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -23.43500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -15.15075 REMARK 400 REMARK 400 COMPOUND REMARK 400 BR HAS ZERO OCCUPANCY IN 4BF. THE AUTHORS COLLECTED DATA FROM THE REMARK 400 SINGLE CRYSTAL USING THE SYNCHROTRON BEAM TUNED AT THE BROMINE REMARK 400 EDGE. BROMINE IS VERY LABILE UNDER RADIATION AND READILY DEGRADES REMARK 400 UPON REPEATED DATA COLLECTION. THE LAST DATASET IS COLLECTED BY REMARK 400 USING INCREASED EXPOSURE TO ATTAIN DIFFRACTIONS AT THE HIGH- REMARK 400 RESOLUTION SPACE. THIS RESULTS IN OCCUPANCY OF 0 FOR THE MENTIONED REMARK 400 BROMINE. THIS STUDY HAS BEEN CONFIRMED BY MASS SPEC REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 4BF A 2 BR 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 ALA A 6 -71.55 -64.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P6J RELATED DB: PDB REMARK 900 RELATED ID: 4P6L RELATED DB: PDB DBREF 4P6K A 1 26 PDB 4P6K 4P6K 1 26 SEQRES 1 A 26 TYR 4BF 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 HET 4BF A 2 12 HET NH2 A 26 1 HETNAM 4BF 4-BROMO-L-PHENYLALANINE HETNAM NH2 AMINO GROUP HETSYN 4BF P-BROMO-L-PHENYLALANINE FORMUL 1 4BF C9 H10 BR N O2 FORMUL 1 NH2 H2 N HELIX 1 AA1 TYR A 1 TYR A 25 1 25 LINK C TYR A 1 N 4BF A 2 1555 1555 1.33 LINK C 4BF A 2 N LYS A 3 1555 1555 1.33 LINK C TYR A 25 N NH2 A 26 1555 1555 1.33 CRYST1 46.870 46.870 60.603 90.00 90.00 90.00 I 41 2 2 16 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 0.021336 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016501 0.00000