HEADER LIPID BINDING PROTEIN 22-JAN-20 6XVS TITLE HUMAN MYELIN PROTEIN P2 MUTANT P38G, UNLIGANDED COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN P2 PROTEIN; COMPND 3 CHAIN: A, B; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUTANT, PERIPHERAL MEMBRANE PROTEIN, FABP, BETA BARREL, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.RUSKAMO,M.LEHTIMAKI,P.KURSULA REVDAT 5 13-NOV-24 6XVS 1 REMARK REVDAT 4 24-JAN-24 6XVS 1 REMARK REVDAT 3 08-JUL-20 6XVS 1 JRNL REVDAT 2 22-APR-20 6XVS 1 JRNL REVDAT 1 08-APR-20 6XVS 0 JRNL AUTH S.RUSKAMO,O.C.KROKENGEN,J.KOWAL,T.NIEMINEN,M.LEHTIMAKI, JRNL AUTH 2 A.RAASAKKA,V.P.DANDEY,I.VATTULAINEN,H.STAHLBERG,P.KURSULA JRNL TITL CRYO-EM, X-RAY DIFFRACTION, AND ATOMISTIC SIMULATIONS REVEAL JRNL TITL 2 DETERMINANTS FOR THE FORMATION OF A SUPRAMOLECULAR JRNL TITL 3 MYELIN-LIKE PROTEOLIPID LATTICE. JRNL REF J.BIOL.CHEM. V. 295 8692 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32265298 JRNL DOI 10.1074/JBC.RA120.013087 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2247 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 25864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 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) : 32.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.79 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 2277 REMARK 3 ANGLE : 1.167 3056 REMARK 3 CHIRALITY : 0.063 349 REMARK 3 PLANARITY : 0.007 385 REMARK 3 DIHEDRAL : 15.261 1410 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 6XVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106406. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 1.03 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25915 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 21.8000 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 (%) : 58.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57600 REMARK 200 FOR SHELL : 2.200 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: 2WUT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 1000, 0.1 M CITRATE PH 5.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 27.77000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.77000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.74500 REMARK 290 SMTRY3 4 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 205 O HOH A 329 2.08 REMARK 500 O HOH B 302 O HOH B 465 2.11 REMARK 500 OG1 THR A 56 O HOH A 201 2.14 REMARK 500 OE1 GLU B 71 O HOH B 301 2.17 REMARK 500 O HOH B 476 O HOH B 481 2.19 REMARK 500 O HOH A 262 O HOH A 273 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 37 75.46 39.28 REMARK 500 LYS A 120 -121.20 57.50 REMARK 500 ASN B 34 -121.72 71.17 REMARK 500 ALA B 36 72.22 -105.43 REMARK 500 LYS B 120 -128.04 57.28 REMARK 500 REMARK 500 REMARK: NULL 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 A 366 DISTANCE = 6.21 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6B RELATED DB: PDB REMARK 900 LIGAND COMPLEX DBREF 6XVS A 0 131 UNP P02689 MYP2_HUMAN 1 132 DBREF 6XVS B 0 131 UNP P02689 MYP2_HUMAN 1 132 SEQADV 6XVS GLY A -1 UNP P02689 EXPRESSION TAG SEQADV 6XVS GLY A 38 UNP P02689 PRO 39 ENGINEERED MUTATION SEQADV 6XVS GLY B -1 UNP P02689 EXPRESSION TAG SEQADV 6XVS GLY B 38 UNP P02689 PRO 39 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 GLY 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 CSO LYS MET LYS GLY VAL VAL CYS THR ARG ILE TYR SEQRES 11 A 133 GLU LYS VAL SEQRES 1 B 133 GLY MET SER ASN LYS PHE LEU GLY THR TRP LYS LEU VAL SEQRES 2 B 133 SER SER GLU ASN PHE ASP ASP TYR MET LYS ALA LEU GLY SEQRES 3 B 133 VAL GLY LEU ALA THR ARG LYS LEU GLY ASN LEU ALA LYS SEQRES 4 B 133 GLY THR VAL ILE ILE SER LYS LYS GLY ASP ILE ILE THR SEQRES 5 B 133 ILE ARG THR GLU SER THR PHE LYS ASN THR GLU ILE SER SEQRES 6 B 133 PHE LYS LEU GLY GLN GLU PHE GLU GLU THR THR ALA ASP SEQRES 7 B 133 ASN ARG LYS THR LYS SER ILE VAL THR LEU GLN ARG GLY SEQRES 8 B 133 SER LEU ASN GLN VAL GLN ARG TRP ASP GLY LYS GLU THR SEQRES 9 B 133 THR ILE LYS ARG LYS LEU VAL ASN GLY LYS MET VAL ALA SEQRES 10 B 133 GLU CSO LYS MET LYS GLY VAL VAL CYS THR ARG ILE TYR SEQRES 11 B 133 GLU LYS VAL MODRES 6XVS CSO A 117 CYS MODIFIED RESIDUE MODRES 6XVS CSO B 117 CYS MODIFIED RESIDUE HET CSO A 117 12 HET CSO B 117 11 HET GOL B 201 14 HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *347(H2 O) HELIX 1 AA1 SER A 1 LEU A 5 5 5 HELIX 2 AA2 ASN A 15 LEU A 23 1 9 HELIX 3 AA3 GLY A 26 LYS A 37 1 12 HELIX 4 AA4 SER B 1 LEU B 5 5 5 HELIX 5 AA5 ASN B 15 GLY B 24 1 10 HELIX 6 AA6 GLY B 26 GLY B 33 1 8 SHEET 1 AA110 THR A 60 PHE A 64 0 SHEET 2 AA110 ILE A 48 GLU A 54 -1 N ILE A 49 O PHE A 64 SHEET 3 AA110 THR A 39 LYS A 45 -1 N ILE A 41 O ARG A 52 SHEET 4 AA110 GLY A 6 GLU A 14 -1 N TRP A 8 O VAL A 40 SHEET 5 AA110 VAL A 122 VAL A 131 -1 O ILE A 127 N VAL A 11 SHEET 6 AA110 LYS A 112 MET A 119 -1 N ALA A 115 O ARG A 126 SHEET 7 AA110 LYS A 100 VAL A 109 -1 N LYS A 105 O GLU A 116 SHEET 8 AA110 SER A 90 TRP A 97 -1 N TRP A 97 O LYS A 100 SHEET 9 AA110 LYS A 79 GLN A 87 -1 N THR A 85 O ASN A 92 SHEET 10 AA110 PHE A 70 THR A 73 -1 N PHE A 70 O SER A 82 SHEET 1 AA210 THR B 60 PHE B 64 0 SHEET 2 AA210 ILE B 48 GLU B 54 -1 N THR B 53 O THR B 60 SHEET 3 AA210 THR B 39 LYS B 45 -1 N ILE B 41 O ARG B 52 SHEET 4 AA210 GLY B 6 GLU B 14 -1 N TRP B 8 O VAL B 40 SHEET 5 AA210 VAL B 122 LYS B 130 -1 O ILE B 127 N VAL B 11 SHEET 6 AA210 LYS B 112 MET B 119 -1 N CSO B 117 O CYS B 124 SHEET 7 AA210 LYS B 100 VAL B 109 -1 N VAL B 109 O LYS B 112 SHEET 8 AA210 SER B 90 TRP B 97 -1 N GLN B 93 O ILE B 104 SHEET 9 AA210 LYS B 79 GLN B 87 -1 N THR B 85 O ASN B 92 SHEET 10 AA210 PHE B 70 THR B 73 -1 N GLU B 72 O THR B 80 LINK C GLU A 116 N CSO A 117 1555 1555 1.32 LINK C CSO A 117 N LYS A 118 1555 1555 1.32 LINK C AGLU B 116 N CSO B 117 1555 1555 1.33 LINK C BGLU B 116 N CSO B 117 1555 1555 1.33 LINK C CSO B 117 N LYS B 118 1555 1555 1.32 CISPEP 1 GLY B 33 ASN B 34 0 3.04 SITE 1 AC1 3 GLU A 69 GLU A 71 ARG B 88 CRYST1 55.540 65.490 82.230 90.00 90.00 90.00 P 21 21 21 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 0.018005 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012161 0.00000