HEADER STRUCTURAL PROTEIN 10-NOV-14 4D6A TITLE HUMAN MYELIN PROTEIN P2 AFTER NEUTRON SCATTERING EXPERIMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELIN P2 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PERIPHERAL MYELIN PROTEIN 2, MYELIN PROTEIN P2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTH27 KEYWDS STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LAULUMAA,F.NATALI,P.KURSULA REVDAT 5 16-OCT-24 4D6A 1 REMARK REVDAT 4 20-DEC-23 4D6A 1 REMARK LINK REVDAT 3 17-JAN-18 4D6A 1 REMARK REVDAT 2 24-JUN-15 4D6A 1 JRNL REVDAT 1 20-MAY-15 4D6A 0 JRNL AUTH S.LAULUMAA,T.NIEMINEN,M.LEHTIMAKI,S.AGGARWAL,M.SIMONS, JRNL AUTH 2 M.M.KOZA,I.VATTULAINEN,P.KURSULA,F.NATALI JRNL TITL DYNAMICS OF THE PERIPHERAL MEMBRANE PROTEIN P2 FROM HUMAN JRNL TITL 2 MYELIN MEASURED BY NEUTRON SCATTERING-A COMPARISON BETWEEN JRNL TITL 3 WILD-TYPE PROTEIN AND A HINGE MUTANT. JRNL REF PLOS ONE V. 10 28954 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26068118 JRNL DOI 10.1371/JOURNAL.PONE.0128954 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30806 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 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 29.0076 - 3.2234 0.98 2835 149 0.1500 0.1730 REMARK 3 2 3.2234 - 2.5590 1.00 2726 143 0.1529 0.1794 REMARK 3 3 2.5590 - 2.2357 1.00 2680 141 0.1380 0.1869 REMARK 3 4 2.2357 - 2.0313 1.00 2669 141 0.1249 0.1724 REMARK 3 5 2.0313 - 1.8857 1.00 2649 140 0.1172 0.1718 REMARK 3 6 1.8857 - 1.7746 1.00 2629 137 0.1214 0.1543 REMARK 3 7 1.7746 - 1.6857 1.00 2630 139 0.1326 0.1822 REMARK 3 8 1.6857 - 1.6123 1.00 2620 138 0.1537 0.2118 REMARK 3 9 1.6123 - 1.5503 1.00 2620 138 0.1733 0.2090 REMARK 3 10 1.5503 - 1.4968 1.00 2618 138 0.2115 0.3009 REMARK 3 11 1.4968 - 1.4500 1.00 2590 136 0.2654 0.3232 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 1164 REMARK 3 ANGLE : 1.324 1565 REMARK 3 CHIRALITY : 0.070 177 REMARK 3 PLANARITY : 0.005 196 REMARK 3 DIHEDRAL : 19.981 468 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 4D6A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1290062275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9444 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30872 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 1.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 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 2WUT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 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 50.33000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.83500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.16500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.83500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.49500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.16500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.49500 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 50.33000 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 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 2128 O HOH A 2133 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2029 O HOH A 2177 3455 2.06 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 1134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1133 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D6B RELATED DB: PDB REMARK 900 HUMAN MYELIN PROTEIN P2, MUTANT P38G DBREF 4D6A A 0 131 UNP P02689 MYP2_HUMAN 1 132 SEQADV 4D6A GLY A -1 UNP P02689 EXPRESSION TAG 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 CSO LYS MET LYS GLY VAL VAL CSO THR ARG ILE TYR SEQRES 11 A 133 GLU LYS VAL MODRES 4D6A CSO A 117 CYS S-HYDROXYCYSTEINE MODRES 4D6A CSO A 124 CYS S-HYDROXYCYSTEINE HET CSO A 117 12 HET CSO A 124 11 HET CIT A1132 18 HET CIT A1133 18 HET PLM A1134 49 HETNAM CSO S-HYDROXYCYSTEINE HETNAM CIT CITRIC ACID HETNAM PLM PALMITIC ACID FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 2 CIT 2(C6 H8 O7) FORMUL 4 PLM C16 H32 O2 FORMUL 5 HOH *180(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 LINK C GLU A 116 N ACSO A 117 1555 1555 1.33 LINK C ACSO A 117 N LYS A 118 1555 1555 1.33 SITE 1 AC1 6 ASP A 76 ARG A 106 ARG A 126 TYR A 128 SITE 2 AC1 6 HOH A2086 HOH A2158 SITE 1 AC2 13 VAL A 11 SER A 12 GLY A 26 LEU A 27 SITE 2 AC2 13 ALA A 28 HOH A2026 HOH A2028 HOH A2029 SITE 3 AC2 13 HOH A2030 HOH A2059 HOH A2113 HOH A2177 SITE 4 AC2 13 HOH A2179 SITE 1 AC3 14 LYS A 9 ALA A 36 LYS A 37 SER A 55 SITE 2 AC3 14 THR A 56 LEU A 86 ARG A 88 GLY A 89 SITE 3 AC3 14 HOH A2001 HOH A2002 HOH A2003 HOH A2090 SITE 4 AC3 14 HOH A2135 HOH A2180 CRYST1 57.670 57.670 100.660 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 0.017340 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009934 0.00000