PDB Short entry for 5EH4 HEADER MEMBRANE PROTEIN 28-OCT-15 5EH4 TITLE CRYSTAL STRUCTURE OF THE GLYCOPHORIN A TRANSMEMBRANE DIMER IN LIPIDIC TITLE 2 CUBIC PHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOPHORIN-A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 89-117; COMPND 5 SYNONYM: MN SIALOGLYCOPROTEIN,PAS-2,SIALOGLYCOPROTEIN ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: ERYTHROCYTE; SOURCE 6 GENE: GYPA, GPA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRPLE KEYWDS RECEPTOR, LIPIDIC CUBIC PHASE, PEPTIDES, TRANSMEMBRANE, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.CALL,M.E.CALL,R.TRENKER REVDAT 6 27-SEP-23 5EH4 1 REMARK REVDAT 5 01-JAN-20 5EH4 1 REMARK REVDAT 4 17-JAN-18 5EH4 1 REMARK REVDAT 3 20-SEP-17 5EH4 1 REMARK REVDAT 2 06-JAN-16 5EH4 1 JRNL REVDAT 1 23-DEC-15 5EH4 0 JRNL AUTH R.TRENKER,M.E.CALL,M.J.CALL JRNL TITL CRYSTAL STRUCTURE OF THE GLYCOPHORIN A TRANSMEMBRANE DIMER JRNL TITL 2 IN LIPIDIC CUBIC PHASE. JRNL REF J.AM.CHEM.SOC. V. 137 15676 2015 JRNL REFN ESSN 1520-5126 JRNL PMID 26642914 JRNL DOI 10.1021/JACS.5B11354 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 3515 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.440 REMARK 3 FREE R VALUE TEST SET COUNT : 367 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 21.5705 - 4.0470 0.90 1102 128 0.2292 0.2233 REMARK 3 2 4.0470 - 3.2157 0.90 1046 122 0.2234 0.2445 REMARK 3 3 3.2157 - 2.8102 0.86 996 116 0.2362 0.3785 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.30 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 : 0.002 952 REMARK 3 ANGLE : 0.638 1281 REMARK 3 CHIRALITY : 0.020 169 REMARK 3 PLANARITY : 0.004 150 REMARK 3 DIHEDRAL : 12.222 346 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 5EH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3581 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 35.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.36020 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.86200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.9_1692 REMARK 200 STARTING MODEL: 5EH6 REMARK 200 REMARK 200 REMARK: DISCOID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V)PEG 8000, 0.1 M SODIUM HEPES REMARK 280 PH 7.5 10 MM TRIS-HCL PH 8, 40 MM NACL, LIPIDIC CUBIC PHASE, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.13967 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.27933 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 86.27933 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.13967 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 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: 1110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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: 890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 B 71 69.69 -60.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OLB A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EH6 RELATED DB: PDB DBREF 5EH4 A 70 98 UNP P02724 GLPA_HUMAN 89 117 DBREF 5EH4 B 70 98 UNP P02724 GLPA_HUMAN 89 117 DBREF 5EH4 C 70 98 UNP P02724 GLPA_HUMAN 89 117 DBREF 5EH4 D 70 98 UNP P02724 GLPA_HUMAN 89 117 SEQADV 5EH4 ILE A 81 UNP P02724 MET 100 ENGINEERED MUTATION SEQADV 5EH4 ILE B 81 UNP P02724 MET 100 ENGINEERED MUTATION SEQADV 5EH4 ILE C 81 UNP P02724 MET 100 ENGINEERED MUTATION SEQADV 5EH4 ILE D 81 UNP P02724 MET 100 ENGINEERED MUTATION SEQRES 1 A 30 GLU PRO GLU ILE THR LEU ILE ILE PHE GLY VAL ILE ALA SEQRES 2 A 30 GLY VAL ILE GLY THR ILE LEU LEU ILE SER TYR GLY ILE SEQRES 3 A 30 ARG ARG LEU SCH SEQRES 1 B 30 GLU PRO GLU ILE THR LEU ILE ILE PHE GLY VAL ILE ALA SEQRES 2 B 30 GLY VAL ILE GLY THR ILE LEU LEU ILE SER TYR GLY ILE SEQRES 3 B 30 ARG ARG LEU SCH SEQRES 1 C 30 GLU PRO GLU ILE THR LEU ILE ILE PHE GLY VAL ILE ALA SEQRES 2 C 30 GLY VAL ILE GLY THR ILE LEU LEU ILE SER TYR GLY ILE SEQRES 3 C 30 ARG ARG LEU SCH SEQRES 1 D 30 GLU PRO GLU ILE THR LEU ILE ILE PHE GLY VAL ILE ALA SEQRES 2 D 30 GLY VAL ILE GLY THR ILE LEU LEU ILE SER TYR GLY ILE SEQRES 3 D 30 ARG ARG LEU SCH MODRES 5EH4 SCH A 99 MODIFIED RESIDUE MODRES 5EH4 SCH B 99 MODIFIED RESIDUE MODRES 5EH4 SCH C 99 MODIFIED RESIDUE MODRES 5EH4 SCH D 99 MODIFIED RESIDUE HET SCH A 99 9 HET SCH B 99 9 HET SCH C 99 9 HET SCH D 99 9 HET OLB A 101 25 HETNAM SCH S-METHYL-THIO-CYSTEINE HETNAM OLB (2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE FORMUL 1 SCH 4(C4 H9 N O2 S2) FORMUL 5 OLB C21 H40 O4 HELIX 1 AA1 GLU A 70 ARG A 96 1 27 HELIX 2 AA2 ILE B 73 ARG B 96 1 24 HELIX 3 AA3 PRO C 71 ARG C 97 1 27 HELIX 4 AA4 GLU D 72 SCH D 99 1 28 LINK C LEU A 98 N SCH A 99 1555 1555 1.33 LINK C LEU B 98 N SCH B 99 1555 1555 1.33 LINK C LEU C 98 N SCH C 99 1555 1555 1.33 LINK C LEU D 98 N SCH D 99 1555 1555 1.33 SITE 1 AC1 6 PHE A 78 VAL B 84 THR C 74 VAL C 84 SITE 2 AC1 6 ALA D 82 LEU D 90 CRYST1 43.195 43.195 129.419 90.00 90.00 120.00 P 31 1 2 24 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 0.023151 0.013366 0.000000 0.00000 SCALE2 0.000000 0.026732 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007727 0.00000