HEADER LIPID BINDING PROTEIN 21-JUN-19 6S2M TITLE PERDEUTERATED HUMAN MYELIN PROTEIN P2 AT 0.72-A RESOLUTION 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 FABP, BETA BARREL, DEUTERATION, FATTY ACID, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LAULUMAA,P.KURSULA REVDAT 4 20-NOV-24 6S2M 1 REMARK REVDAT 3 24-JAN-24 6S2M 1 REMARK REVDAT 2 04-SEP-19 6S2M 1 JRNL REVDAT 1 28-AUG-19 6S2M 0 JRNL AUTH S.LAULUMAA,P.KURSULA JRNL TITL SUB-ATOMIC RESOLUTION CRYSTAL STRUCTURES REVEAL CONSERVED JRNL TITL 2 GEOMETRIC OUTLIERS AT FUNCTIONAL SITES. JRNL REF MOLECULES V. 24 2019 JRNL REFN ESSN 1420-3049 JRNL PMID 31443388 JRNL DOI 10.3390/MOLECULES24173044 REMARK 2 REMARK 2 RESOLUTION. 0.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 0.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 162057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.104 REMARK 3 R VALUE (WORKING SET) : 0.104 REMARK 3 FREE R VALUE : 0.111 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1621 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 27.8548 - 1.6482 0.98 14761 149 0.1103 0.1106 REMARK 3 2 1.6482 - 1.3082 0.99 14683 150 0.0908 0.1002 REMARK 3 3 1.3082 - 1.1429 0.98 14483 144 0.0603 0.0733 REMARK 3 4 1.1429 - 1.0384 0.97 14230 143 0.0555 0.0660 REMARK 3 5 1.0384 - 0.9639 0.97 14314 145 0.0683 0.0815 REMARK 3 6 0.9639 - 0.9071 0.95 13923 139 0.0943 0.1230 REMARK 3 7 0.9071 - 0.8617 0.96 14093 143 0.1244 0.1367 REMARK 3 8 0.8617 - 0.8242 0.94 13735 140 0.1854 0.2017 REMARK 3 9 0.8242 - 0.7924 0.94 13879 141 0.2364 0.2636 REMARK 3 10 0.7924 - 0.7651 0.92 13424 135 0.2892 0.3040 REMARK 3 11 0.7651 - 0.7412 0.75 10958 112 0.3297 0.2865 REMARK 3 12 0.7412 - 0.7200 0.54 7953 80 0.3739 0.3729 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.00 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 : 0.020 1682 REMARK 3 ANGLE : 1.763 2279 REMARK 3 CHIRALITY : 0.107 253 REMARK 3 PLANARITY : 0.012 300 REMARK 3 DIHEDRAL : 20.687 695 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 6S2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292103034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7443 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 : 162608 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.720 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.21400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 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 (%): 41.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG6000, 0.1 M SODIUM CITRATE, PH REMARK 280 5, PH 4.25, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.09000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.09000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.10500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 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 454 O HOH A 507 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 78 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES 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 ASP A 98 -126.08 55.94 REMARK 500 LYS A 120 -136.92 50.25 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 529 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 530 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 531 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A 532 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH A 533 DISTANCE = 8.57 ANGSTROMS 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 DBREF 6S2M A 0 131 UNP P02689 MYP2_HUMAN 1 132 SEQADV 6S2M 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 6S2M CSO A 117 CYS MODIFIED RESIDUE MODRES 6S2M CSO A 124 CYS MODIFIED RESIDUE HET CSO A 117 20 HET CSO A 124 20 HET PLM A 201 49 HET VCA A 202 53 HETNAM CSO S-HYDROXYCYSTEINE HETNAM PLM PALMITIC ACID HETNAM VCA VACCENIC ACID HETSYN VCA (11E)-OCTADEC-11-ENOIC ACID FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 2 PLM C16 H32 O2 FORMUL 3 VCA C18 H34 O2 FORMUL 4 HOH *233(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 ALA A 36 1 11 SHEET 1 AA110 ASN A 59 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 GLY A 6 O ILE A 42 SHEET 5 AA110 VAL A 122 LYS A 130 -1 O ILE A 127 N SER A 12 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 GLN A 93 O ILE A 104 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 LINK C AGLU A 116 N ACSO A 117 1555 1555 1.33 LINK C BGLU A 116 N BCSO A 117 1555 1555 1.30 LINK C ACSO A 117 N ALYS A 118 1555 1555 1.32 LINK C BCSO A 117 N BLYS A 118 1555 1555 1.31 LINK C VAL A 123 N ACSO A 124 1555 1555 1.32 LINK C VAL A 123 N BCSO A 124 1555 1555 1.35 LINK C ACSO A 124 N ATHR A 125 1555 1555 1.34 LINK C BCSO A 124 N BTHR A 125 1555 1555 1.35 SITE 1 AC1 10 MET A 20 GLY A 33 SER A 55 ALA A 75 SITE 2 AC1 10 ARG A 106 ARG A 126 TYR A 128 VCA A 202 SITE 3 AC1 10 HOH A 338 HOH A 382 SITE 1 AC2 16 PHE A 16 MET A 20 THR A 29 GLY A 33 SITE 2 AC2 16 THR A 53 SER A 55 LYS A 58 ALA A 75 SITE 3 AC2 16 ASP A 76 ARG A 106 CSO A 117 ARG A 126 SITE 4 AC2 16 TYR A 128 PLM A 201 HOH A 338 HOH A 382 CRYST1 112.180 36.210 31.110 90.00 97.03 90.00 C 1 2 1 4 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 0.008914 0.000000 0.001100 0.00000 SCALE2 0.000000 0.027617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032388 0.00000