PDB Short entry for 5LDL HEADER VIRAL PROTEIN 27-JUN-16 5LDL TITLE MYRISTOYLATED T41I/T78I MUTANT OF M-PMV MATRIX PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYRISTOYLATED M-PMV MATRIX PROTEIN MUTANT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CORE POLYPROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MASON-PFIZER MONKEY VIRUS; SOURCE 3 ORGANISM_COMMON: MPMV; SOURCE 4 ORGANISM_TAXID: 11855; SOURCE 5 GENE: GAG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MATRIX PROTEIN, M-PMV, RETROVIRUS, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR T.KROUPA,R.HRABAL REVDAT 6 14-JUN-23 5LDL 1 REMARK REVDAT 5 08-MAY-19 5LDL 1 REMARK REVDAT 4 30-NOV-16 5LDL 1 JRNL REVDAT 3 19-OCT-16 5LDL 1 JRNL REVDAT 2 28-SEP-16 5LDL 1 REVDAT 1 27-JUL-16 5LDL 0 SPRSDE 27-JUL-16 5LDL 2MXI JRNL AUTH T.KROUPA,H.LANGEROVA,M.DOLEZAL,J.PRCHAL,V.SPIWOK,E.HUNTER, JRNL AUTH 2 M.RUMLOVA,R.HRABAL,T.RUML JRNL TITL MEMBRANE INTERACTIONS OF THE MASON-PFIZER MONKEY VIRUS JRNL TITL 2 MATRIX PROTEIN AND ITS BUDDING DEFICIENT MUTANTS. JRNL REF J.MOL.BIOL. V. 428 4708 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27725181 JRNL DOI 10.1016/J.JMB.2016.10.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CCPNMR ANALYSIS REMARK 3 AUTHORS : CCPN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000525. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 600 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] REMARK 210 MYRISTOYLATED RETROVIRAL MATRIX REMARK 210 PROTEIN, 100 MM PHOSPHATE, 300 REMARK 210 MM SODIUM CHORIDE, 5 MM DTT, 90% REMARK 210 H2O/10% D2O; 400 MM [U-15N] REMARK 210 MYRISTOYLATED RETROVIRAL MATRIX REMARK 210 PROTEIN, 50 MM PHOSPHATE, 150 MM REMARK 210 SODIUM CHORIDE, 5 MM DTT, 10 MG/ REMARK 210 ML PF1 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 2D 1H-15N HSQC REMARK 210 IPAP; 3D HNCACB; 3D HCCH-TOCSY; REMARK 210 3D 1H-13C NOESY; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, XPLOR-NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 HZ1 LYS A 93 H101 MYR A 201 1.32 REMARK 500 HZ2 LYS A 93 H122 MYR A 201 1.34 REMARK 500 N GLY A 2 C2 MYR A 201 1.94 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 1 GLU A 4 -6.58 -50.10 REMARK 500 1 LYS A 25 -165.60 -51.67 REMARK 500 1 GLU A 48 -78.44 -115.80 REMARK 500 1 VAL A 75 102.61 -46.64 REMARK 500 1 TYR A 82 179.91 -59.71 REMARK 500 1 TRP A 83 -65.58 68.31 REMARK 500 1 GLU A 94 -9.49 -47.46 REMARK 500 1 ASN A 96 69.57 162.90 REMARK 500 1 SER A 112 -161.01 -71.63 REMARK 500 1 SER A 114 23.07 -164.03 REMARK 500 1 GLN A 115 -121.06 -110.53 REMARK 500 1 GLU A 119 94.11 54.63 REMARK 500 2 GLU A 4 -8.72 -49.67 REMARK 500 2 LYS A 25 -167.56 -51.82 REMARK 500 2 CYS A 42 77.61 -118.27 REMARK 500 2 GLU A 48 -78.16 -99.28 REMARK 500 2 VAL A 75 100.92 -44.41 REMARK 500 2 TYR A 82 162.07 -49.16 REMARK 500 2 TRP A 83 -60.39 68.83 REMARK 500 2 GLU A 94 -11.21 -46.11 REMARK 500 2 ASN A 96 67.67 162.02 REMARK 500 2 ALA A 102 -17.23 -48.60 REMARK 500 2 LYS A 111 -164.36 -54.02 REMARK 500 2 GLU A 119 -166.34 48.14 REMARK 500 3 GLU A 4 -11.31 -49.45 REMARK 500 3 LYS A 25 -167.24 -53.57 REMARK 500 3 CYS A 42 77.69 -117.86 REMARK 500 3 GLU A 48 -76.13 -98.65 REMARK 500 3 VAL A 75 100.57 -44.32 REMARK 500 3 TRP A 83 -65.38 64.40 REMARK 500 3 GLU A 94 -5.00 -52.99 REMARK 500 3 ASN A 96 60.55 165.02 REMARK 500 3 PRO A 97 -156.72 -91.24 REMARK 500 3 ALA A 102 -18.90 -49.20 REMARK 500 4 GLU A 4 -10.85 -48.34 REMARK 500 4 VAL A 24 61.91 -62.66 REMARK 500 4 LYS A 25 -163.74 36.14 REMARK 500 4 CYS A 42 78.44 -118.94 REMARK 500 4 GLU A 48 -76.70 -103.04 REMARK 500 4 VAL A 75 100.42 -44.15 REMARK 500 4 TYR A 82 173.27 -59.82 REMARK 500 4 TRP A 83 -72.09 73.46 REMARK 500 4 GLU A 94 -5.77 -55.81 REMARK 500 4 ASN A 96 61.45 166.92 REMARK 500 4 PRO A 97 -158.17 -90.91 REMARK 500 4 ALA A 102 -18.76 -49.87 REMARK 500 4 LYS A 111 -163.78 -174.57 REMARK 500 4 GLU A 119 18.47 51.85 REMARK 500 5 GLU A 4 -18.64 -39.05 REMARK 500 5 LYS A 25 -169.48 -51.06 REMARK 500 REMARK 500 THIS ENTRY HAS 375 RAMACHANDRAN OUTLIERS. 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 MYR A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25411 RELATED DB: BMRB REMARK 900 RELATED ID: 34015 RELATED DB: BMRB DBREF 5LDL A 2 118 UNP P07567 GAG_MPMV 2 118 SEQADV 5LDL ILE A 41 UNP P07567 THR 41 ENGINEERED MUTATION SEQADV 5LDL ILE A 78 UNP P07567 THR 78 ENGINEERED MUTATION SEQADV 5LDL GLU A 119 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 120 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 121 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 122 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 123 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 124 UNP P07567 EXPRESSION TAG SEQADV 5LDL HIS A 125 UNP P07567 EXPRESSION TAG SEQRES 1 A 124 GLY GLN GLU LEU SER GLN HIS GLU ARG TYR VAL GLU GLN SEQRES 2 A 124 LEU LYS GLN ALA LEU LYS THR ARG GLY VAL LYS VAL LYS SEQRES 3 A 124 TYR ALA ASP LEU LEU LYS PHE PHE ASP PHE VAL LYS ASP SEQRES 4 A 124 ILE CYS PRO TRP PHE PRO GLN GLU GLY THR ILE ASP ILE SEQRES 5 A 124 LYS ARG TRP ARG ARG VAL GLY ASP CYS PHE GLN ASP TYR SEQRES 6 A 124 TYR ASN THR PHE GLY PRO GLU LYS VAL PRO VAL ILE ALA SEQRES 7 A 124 PHE SER TYR TRP ASN LEU ILE LYS GLU LEU ILE ASP LYS SEQRES 8 A 124 LYS GLU VAL ASN PRO GLN VAL MET ALA ALA VAL ALA GLN SEQRES 9 A 124 THR GLU GLU ILE LEU LYS SER ASN SER GLN THR ASP LEU SEQRES 10 A 124 GLU HIS HIS HIS HIS HIS HIS HET MYR A 201 42 HETNAM MYR MYRISTIC ACID FORMUL 2 MYR C14 H28 O2 HELIX 1 AA1 GLU A 4 ARG A 22 1 19 HELIX 2 AA2 TYR A 28 CYS A 42 1 15 HELIX 3 AA3 ILE A 53 PHE A 70 1 18 HELIX 4 AA4 VAL A 77 GLU A 94 1 18 HELIX 5 AA5 PRO A 97 GLU A 107 1 11 LINK N GLY A 2 C1 MYR A 201 1555 1555 1.33 SITE 1 AC1 6 GLY A 2 HIS A 8 LYS A 33 ILE A 51 SITE 2 AC1 6 LYS A 93 GLN A 98 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000