HEADER LIPID BINDING PROTEIN 11-FEB-17 5N4M TITLE HUMAN MYELIN PROTEIN P2, MUTANT I43N 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PMP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FATTY ACID BINDING PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.RUSKAMO,P.KURSULA REVDAT 2 17-JAN-24 5N4M 1 REMARK REVDAT 1 09-AUG-17 5N4M 0 JRNL AUTH S.RUSKAMO,T.NIEMINEN,C.K.KRISTIANSEN,G.H.VATNE,A.BAUMANN, JRNL AUTH 2 E.I.HALLIN,A.RAASAKKA,P.JOENSUU,U.BERGMANN,I.VATTULAINEN, JRNL AUTH 3 P.KURSULA JRNL TITL MOLECULAR MECHANISMS OF CHARCOT-MARIE-TOOTH NEUROPATHY JRNL TITL 2 LINKED TO MUTATIONS IN HUMAN MYELIN PROTEIN P2. JRNL REF SCI REP V. 7 6510 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28747762 JRNL DOI 10.1038/S41598-017-06781-0 REMARK 2 REMARK 2 RESOLUTION. 1.59 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 29399 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 45.9790 - 3.8315 1.00 2167 158 0.1403 0.1720 REMARK 3 2 3.8315 - 3.0414 1.00 2050 148 0.1627 0.1945 REMARK 3 3 3.0414 - 2.6570 1.00 2019 146 0.1974 0.2436 REMARK 3 4 2.6570 - 2.4140 1.00 1976 143 0.2016 0.1947 REMARK 3 5 2.4140 - 2.2410 1.00 1976 144 0.1952 0.1845 REMARK 3 6 2.2410 - 2.1089 1.00 1972 144 0.1877 0.2439 REMARK 3 7 2.1089 - 2.0033 1.00 1978 144 0.2040 0.2365 REMARK 3 8 2.0033 - 1.9161 0.99 1946 142 0.2302 0.3051 REMARK 3 9 1.9161 - 1.8423 0.99 1957 139 0.2494 0.2783 REMARK 3 10 1.8423 - 1.7787 0.99 1951 141 0.2390 0.2819 REMARK 3 11 1.7787 - 1.7231 1.00 1940 142 0.2605 0.3323 REMARK 3 12 1.7231 - 1.6739 0.99 1917 140 0.3322 0.3418 REMARK 3 13 1.6739 - 1.6298 0.99 1927 140 0.3848 0.3678 REMARK 3 14 1.6298 - 1.5900 0.84 1633 119 0.4769 0.4562 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.80 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 : 0.007 1204 REMARK 3 ANGLE : 1.013 1616 REMARK 3 CHIRALITY : 0.040 180 REMARK 3 PLANARITY : 0.004 205 REMARK 3 DIHEDRAL : 13.231 499 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 5N4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 45.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 3.00000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.700 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: 4BVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 M DL-MALIC ACID, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 50.54200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.49850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.49850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.27100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.49850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.49850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.81300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.49850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.49850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.27100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.49850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.49850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.81300 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 50.54200 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 TOTAL BURIED SURFACE AREA: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 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 376 O HOH A 411 2.14 REMARK 500 O HOH A 381 O HOH A 387 2.15 REMARK 500 O HOH A 304 O HOH A 409 2.16 REMARK 500 OE1 GLU A 15 O HOH A 301 2.19 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue VCA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLT A 203 DBREF 5N4M A 1 132 UNP P02689 MYP2_HUMAN 1 132 SEQADV 5N4M GLY A 0 UNP P02689 EXPRESSION TAG SEQADV 5N4M ASN A 43 UNP P02689 ILE 43 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 ASN 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 A 201 49 HET VCA A 202 53 HET MLT A 203 13 HETNAM PLM PALMITIC ACID HETNAM VCA VACCENIC ACID HETNAM MLT D-MALATE HETSYN VCA (11E)-OCTADEC-11-ENOIC ACID HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID FORMUL 2 PLM C16 H32 O2 FORMUL 3 VCA C18 H34 O2 FORMUL 4 MLT C4 H6 O5 FORMUL 5 HOH *134(H2 O) HELIX 1 AA1 SER A 2 LEU A 6 5 5 HELIX 2 AA2 ASN A 16 GLY A 25 1 10 HELIX 3 AA3 GLY A 27 ALA A 37 1 11 SHEET 1 AA110 THR A 61 PHE A 65 0 SHEET 2 AA110 ILE A 49 GLU A 55 -1 N ILE A 50 O PHE A 65 SHEET 3 AA110 THR A 40 LYS A 46 -1 N THR A 40 O GLU A 55 SHEET 4 AA110 GLY A 7 GLU A 15 -1 N TRP A 9 O VAL A 41 SHEET 5 AA110 VAL A 123 LYS A 131 -1 O ILE A 128 N VAL A 12 SHEET 6 AA110 LYS A 113 MET A 120 -1 N ALA A 116 O ARG A 127 SHEET 7 AA110 LYS A 101 VAL A 110 -1 N LYS A 108 O VAL A 115 SHEET 8 AA110 SER A 91 TRP A 98 -1 N LEU A 92 O ARG A 107 SHEET 9 AA110 LYS A 80 GLN A 88 -1 N THR A 86 O ASN A 93 SHEET 10 AA110 PHE A 71 THR A 74 -1 N PHE A 71 O SER A 83 SITE 1 AC1 9 LEU A 24 GLY A 34 ASP A 77 ARG A 107 SITE 2 AC1 9 ARG A 127 TYR A 129 VCA A 202 HOH A 306 SITE 3 AC1 9 HOH A 356 SITE 1 AC2 11 GLY A 34 PRO A 39 THR A 54 ALA A 76 SITE 2 AC2 11 ASP A 77 ARG A 107 ARG A 127 TYR A 129 SITE 3 AC2 11 PLM A 201 HOH A 306 HOH A 356 SITE 1 AC3 5 LYS A 10 LYS A 38 SER A 56 THR A 57 SITE 2 AC3 5 HOH A 374 CRYST1 64.997 64.997 101.084 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 0.015385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009893 0.00000