PDB Short entry for 2WUT HEADER TRANSPORT 09-OCT-09 2WUT TITLE CRYSTAL STRUCTURE OF HUMAN MYELIN PROTEIN P2 IN COMPLEX WITH PALMITATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN P2 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: PERIPHERAL NERVE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTH27 KEYWDS MYELIN, TRANSPORT, LIPID-BINDING, FATTY ACID BINDING PROTEIN, KEYWDS 2 PERIPHERAL MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.MAJAVA,R.NANEKAR,P.KURSULA REVDAT 2 20-DEC-23 2WUT 1 REMARK REVDAT 1 12-MAY-10 2WUT 0 JRNL AUTH V.MAJAVA,E.POLVERINI,A.MAZZINI,R.NANEKAR,W.KNOLL,J.PETERS, JRNL AUTH 2 F.NATALI,P.BAUMGARTEL,I.KURSULA,P.KURSULA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF HUMAN JRNL TITL 2 PERIPHERAL NERVOUS SYSTEM MYELIN PROTEIN P2. JRNL REF PLOS ONE V. 5 E300 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20421974 JRNL DOI 10.1371/JOURNAL.PONE.0010300 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 19657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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 19.3782 - 3.5327 1.00 2879 152 0.1576 0.1854 REMARK 3 2 3.5327 - 2.8067 1.00 2733 144 0.1497 0.2131 REMARK 3 3 2.8067 - 2.4527 1.00 2678 141 0.1580 0.2037 REMARK 3 4 2.4527 - 2.2288 1.00 2689 141 0.1662 0.2070 REMARK 3 5 2.2288 - 2.0693 0.99 2640 139 0.1743 0.2224 REMARK 3 6 2.0693 - 1.9474 0.99 2626 138 0.1951 0.2712 REMARK 3 7 1.9474 - 1.8500 0.92 2429 128 0.2385 0.2622 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 79.77 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.31950 REMARK 3 B22 (A**2) : 4.31950 REMARK 3 B33 (A**2) : -8.63900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1167 REMARK 3 ANGLE : 1.001 1569 REMARK 3 CHIRALITY : 0.071 179 REMARK 3 PLANARITY : 0.004 196 REMARK 3 DIHEDRAL : 14.899 476 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 2WUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290041371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9334 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19658 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: PDB ENTRY 1YIV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.61000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.16500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.30500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.16500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.16500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.91500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.16500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.16500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.30500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.16500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.16500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.91500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 50.61000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2027 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 6.68 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 1134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1136 DBREF 2WUT A -1 -1 PDB 2WUT 2WUT -1 -1 DBREF 2WUT A 0 131 UNP P02689 MYP2_HUMAN 1 132 SEQRES 1 A 133 GLY MET SER ASN LYS PHE LEU GLY THR TRP LYS LEU VAL SEQRES 2 A 133 SER SER GLU ASN PHE ASP ASP TYR MET LYS ALA LEU GLY SEQRES 3 A 133 VAL GLY LEU ALA THR ARG LYS LEU GLY ASN LEU ALA LYS SEQRES 4 A 133 PRO THR VAL ILE ILE SER LYS LYS GLY ASP ILE ILE THR SEQRES 5 A 133 ILE ARG THR GLU SER THR PHE LYS ASN THR GLU ILE SER SEQRES 6 A 133 PHE LYS LEU GLY GLN GLU PHE GLU GLU THR THR ALA ASP SEQRES 7 A 133 ASN ARG LYS THR LYS SER ILE VAL THR LEU GLN ARG GLY SEQRES 8 A 133 SER LEU ASN GLN VAL GLN ARG TRP ASP GLY LYS GLU THR SEQRES 9 A 133 THR ILE LYS ARG LYS LEU VAL ASN GLY LYS MET VAL ALA SEQRES 10 A 133 GLU CYS LYS MET LYS GLY VAL VAL CYS THR ARG ILE TYR SEQRES 11 A 133 GLU LYS VAL HET PLM A1134 18 HET CL A1135 1 HET GOL A1136 6 HETNAM PLM PALMITIC ACID HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PLM C16 H32 O2 FORMUL 3 CL CL 1- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *275(H2 O) HELIX 1 1 SER A 1 LEU A 5 5 5 HELIX 2 2 ASN A 15 LEU A 23 1 9 HELIX 3 3 GLY A 26 ALA A 36 1 11 SHEET 1 AA10 THR A 60 PHE A 64 0 SHEET 2 AA10 ILE A 48 GLU A 54 -1 O ILE A 49 N PHE A 64 SHEET 3 AA10 THR A 39 LYS A 45 -1 O THR A 39 N GLU A 54 SHEET 4 AA10 GLY A 6 GLU A 14 -1 O GLY A 6 N ILE A 42 SHEET 5 AA10 VAL A 122 LYS A 130 -1 O THR A 125 N GLU A 14 SHEET 6 AA10 LYS A 112 MET A 119 -1 O MET A 113 N TYR A 128 SHEET 7 AA10 LYS A 100 VAL A 109 -1 O THR A 103 N LYS A 118 SHEET 8 AA10 SER A 90 TRP A 97 -1 O LEU A 91 N ARG A 106 SHEET 9 AA10 LYS A 79 GLN A 87 -1 O LYS A 81 N ARG A 96 SHEET 10 AA10 PHE A 70 THR A 73 -1 O PHE A 70 N SER A 82 SITE 1 AC1 10 MET A 20 GLY A 33 SER A 55 ALA A 75 SITE 2 AC1 10 ASP A 76 ARG A 106 ARG A 126 TYR A 128 SITE 3 AC1 10 HOH A2151 HOH A2272 SITE 1 AC2 2 LYS A 37 THR A 56 SITE 1 AC3 6 ASN A 15 ASP A 18 HOH A2062 HOH A2273 SITE 2 AC3 6 HOH A2274 HOH A2275 CRYST1 66.330 66.330 101.220 90.00 90.00 90.00 P 41 21 2 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 0.015076 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009879 0.00000