HEADER TRANSPORT PROTEIN 22-NOV-11 4A8Z TITLE HUMAN MYELIN P2 PROTEIN, K112Q MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN P2 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PERIPHERAL MYELIN PROTEIN 2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PTH27 KEYWDS TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.LEHTIMAKI,S.RUSKAMO,P.KURSULA REVDAT 5 06-NOV-24 4A8Z 1 REMARK REVDAT 4 20-DEC-23 4A8Z 1 REMARK REVDAT 3 08-APR-20 4A8Z 1 REMARK REVDAT 2 17-JUL-19 4A8Z 1 REMARK REVDAT 1 05-DEC-12 4A8Z 0 JRNL AUTH M.LEHTIMAKI,S.RUSKAMO,P.KURSULA JRNL TITL STRUCTURE-FUNCTION RELATIONSHIPS IN THE MYELIN PERIPHERAL JRNL TITL 2 MEMBRANE PROTEIN P2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 21057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1053 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 23.6104 - 3.5986 1.00 2699 143 0.1776 0.1735 REMARK 3 2 3.5986 - 2.8579 1.00 2539 133 0.1706 0.2143 REMARK 3 3 2.8579 - 2.4971 1.00 2517 133 0.1625 0.2143 REMARK 3 4 2.4971 - 2.2690 1.00 2483 130 0.1635 0.1863 REMARK 3 5 2.2690 - 2.1064 1.00 2487 131 0.1713 0.2079 REMARK 3 6 2.1064 - 1.9823 1.00 2440 129 0.1865 0.2319 REMARK 3 7 1.9823 - 1.8831 0.99 2448 129 0.2128 0.2536 REMARK 3 8 1.8831 - 1.8011 0.97 2391 125 0.2696 0.3203 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 : 0.89 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 56.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.72160 REMARK 3 B22 (A**2) : 6.72160 REMARK 3 B33 (A**2) : -13.44320 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 : 0.012 1182 REMARK 3 ANGLE : 1.368 1589 REMARK 3 CHIRALITY : 0.092 179 REMARK 3 PLANARITY : 0.005 193 REMARK 3 DIHEDRAL : 16.261 483 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 4A8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21058 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 1.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 2WUT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 50.59500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.85500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.29750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.85500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.85500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.89250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.85500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.85500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.29750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.85500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.85500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.89250 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 50.59500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.2 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 113 TO GLN REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2109 O HOH A 2137 2.12 REMARK 500 NZ LYS A 105 O HOH A 2169 2.15 REMARK 500 O HOH A 2023 O HOH A 2068 2.15 REMARK 500 O HOH A 2002 O HOH A 2008 2.17 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 PLM A 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1137 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1139 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WUT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MYELIN PROTEIN P2 IN COMPLEX WITH REMARK 900 PALMITATE REMARK 900 RELATED ID: 4A1H RELATED DB: PDB REMARK 900 HUMAN MYELIN P2 PROTEIN, K45S MUTANT REMARK 900 RELATED ID: 4A1Y RELATED DB: PDB REMARK 900 HUMAN MYELIN P2 PROTEIN, K65Q MUTANT DBREF 4A8Z A 0 131 UNP P02689 MYP2_HUMAN 1 132 SEQADV 4A8Z GLY A -1 UNP P02689 EXPRESSION TAG SEQADV 4A8Z GLN A 112 UNP P02689 LYS 113 ENGINEERED MUTATION 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 GLN 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 A1132 34 HET GOL A1133 14 HET GOL A1134 14 HET GOL A1135 14 HET SO4 A1136 5 HET SO4 A1137 5 HET SO4 A1138 5 HET SO4 A1139 5 HETNAM PLM PALMITIC ACID HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PLM C16 H32 O2 FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 SO4 4(O4 S 2-) FORMUL 10 HOH *192(H2 O) HELIX 1 1 SER A 1 LEU A 5 5 5 HELIX 2 2 ASN A 15 GLY A 24 1 10 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 GLN 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 SSBOND 1 CYS A 117 CYS A 124 1555 1555 2.03 SITE 1 AC1 9 GLY A 33 PRO A 38 PHE A 57 ASP A 76 SITE 2 AC1 9 ARG A 106 ARG A 126 TYR A 128 HOH A2099 SITE 3 AC1 9 HOH A2170 SITE 1 AC2 2 ARG A 52 ASN A 59 SITE 1 AC3 3 SER A 1 ASN A 2 LYS A 3 SITE 1 AC4 5 ASN A 15 PHE A 16 ASP A 17 HOH A2035 SITE 2 AC4 5 HOH A2042 SITE 1 AC5 7 ALA A 36 LYS A 37 SER A 55 THR A 56 SITE 2 AC5 7 HOH A2080 HOH A2104 HOH A2191 SITE 1 AC6 3 LEU A 27 ARG A 30 HOH A2069 SITE 1 AC7 3 LYS A 44 LYS A 45 GLY A 46 SITE 1 AC8 6 GLY A -1 ASP A 47 LYS A 65 GLN A 68 SITE 2 AC8 6 HOH A2123 HOH A2192 CRYST1 65.710 65.710 101.190 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 0.015218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009882 0.00000