HEADER LIPID BINDING PROTEIN 04-MAR-21 7NRW TITLE HUMAN MYELIN PROTEIN P2 MUTANT M114T 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 GENE: PMP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTH27 KEYWDS MYELIN, FATTY-ACID BINDING PROTEIN, CHARCOT-MARIE-TOOTH DISEASE, KEYWDS 2 LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.UUSITALO,S.RUSKAMO,P.KURSULA REVDAT 3 31-JAN-24 7NRW 1 REMARK REVDAT 2 15-DEC-21 7NRW 1 JRNL REVDAT 1 01-SEP-21 7NRW 0 JRNL AUTH M.UUSITALO,M.B.KLENOW,S.LAULUMAA,M.P.BLAKELEY,A.C.SIMONSEN, JRNL AUTH 2 S.RUSKAMO,P.KURSULA JRNL TITL HUMAN MYELIN PROTEIN P2: FROM CRYSTALLOGRAPHY TO TIME-LAPSE JRNL TITL 2 MEMBRANE IMAGING AND NEUROPATHY-ASSOCIATED VARIANTS. JRNL REF FEBS J. V. 288 6716 2021 JRNL REFN ISSN 1742-464X JRNL PMID 34138518 JRNL DOI 10.1111/FEBS.16079 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 15042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL 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) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.91 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 : 0.012 1097 REMARK 3 ANGLE : 1.118 1464 REMARK 3 CHIRALITY : 0.057 168 REMARK 3 PLANARITY : 0.006 181 REMARK 3 DIHEDRAL : 19.203 435 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 7NRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114494. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15156 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 4BVM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M SODIUM MALONATE, PH 7, 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 50.46500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.39500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.39500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.23250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.39500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.39500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.69750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.39500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.39500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.23250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.39500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.39500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.69750 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 50.46500 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: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 304 O HOH A 369 1.91 REMARK 500 O HOH A 332 O HOH A 368 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 16 OD1 REMARK 620 2 ASP A 19 OD2 92.0 REMARK 620 3 HOH A 349 O 84.6 92.1 REMARK 620 4 HOH A 356 O 82.2 91.8 166.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 19 OD2 REMARK 620 2 HOH A 314 O 86.7 REMARK 620 3 HOH A 344 O 71.0 98.4 REMARK 620 4 HOH A 356 O 69.0 155.7 74.6 REMARK 620 N 1 2 3 DBREF 7NRW A 1 132 UNP P02689 MYP2_HUMAN 1 132 SEQADV 7NRW GLY A 0 UNP P02689 EXPRESSION TAG SEQADV 7NRW THR A 114 UNP P02689 MET 114 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 LYS THR 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 CL A 202 1 HET MG A 203 1 HET MG A 204 1 HETNAM PLM PALMITIC ACID HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 PLM C16 H32 O2 FORMUL 3 CL CL 1- FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *69(H2 O) HELIX 1 AA1 SER A 2 LEU A 6 5 5 HELIX 2 AA2 ASN A 16 LEU A 24 1 9 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 THR A 54 O THR A 61 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 CYS A 118 O CYS A 125 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 LINK OD1 ASN A 16 MG MG A 203 1555 1555 2.43 LINK OD2 ASP A 19 MG MG A 203 1555 1555 2.11 LINK OD2 ASP A 19 MG MG A 204 1555 1555 2.79 LINK MG MG A 203 O HOH A 349 1555 1555 2.41 LINK MG MG A 203 O HOH A 356 1555 1555 2.22 LINK MG MG A 204 O HOH A 314 1555 1555 2.46 LINK MG MG A 204 O HOH A 344 1555 1555 2.73 LINK MG MG A 204 O HOH A 356 1555 1555 2.70 CRYST1 64.790 64.790 100.930 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 0.015434 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009908 0.00000