PDB Short entry for 5JDP HEADER MEMBRANE PROTEIN 17-APR-16 5JDP TITLE E73V MUTANT OF THE HUMAN VOLTAGE-DEPENDENT ANION CHANNEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HVDAC1,OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1, COMPND 5 PLASMALEMMAL PORIN,PORIN 31HL,PORIN 31HM; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPND 8 SAVPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSENGLEFTSSGSANTETTKVTGSLETKYRWTEYGL COMPND 9 TFTVKWNTDNTLGTEITVEDQLARGLKLTFDSSFSPNTGKKNAKIKTGYKREHINLGCDMDFDIAGPSI COMPND 10 RGALVLGYEGWLAGYQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVN COMPND 11 LAWTAGNSNTRFGIAAKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLG COMPND 12 LGLEFQARS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VDAC1, VDAC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN, STRUCTURE REFINEMENT, SPARSE DATA, PROTEIN KEYWDS 2 DYNAMICS, RELAXATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.JAREMKO,L.JAREMKO,S.VILLINGER,C.SCHMIDT,K.GILLER,C.GRIESINGER, AUTHOR 2 S.BECKER,M.ZWECKSTETTER REVDAT 4 14-JUN-23 5JDP 1 REMARK REVDAT 3 08-MAY-19 5JDP 1 REMARK REVDAT 2 31-AUG-16 5JDP 1 JRNL REVDAT 1 10-AUG-16 5JDP 0 JRNL AUTH M.JAREMKO,S.VILLINGER,C.D.SCHMIDT,C.GRIESINGER,S.BECKER, JRNL AUTH 2 M.ZWECKSTETTER JRNL TITL HIGH-RESOLUTION NMR DETERMINATION OF THE DYNAMIC STRUCTURE JRNL TITL 2 OF MEMBRANE PROTEINS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 10518 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 27461260 JRNL DOI 10.1002/ANIE.201602639 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219859. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM U- 2H, 15N_SAMPLE E73V REMARK 210 MUTANT OF THE VOLTAGE-DEPENDENT REMARK 210 ANION CHANNEL 1, 2 % [U-2H] LDAO, REMARK 210 20 MM [U-2H] TRIS, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : R1 RELAXATION RATE; R2 REMARK 210 RELAXATION RATE; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 900 MHZ; 800 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS, XPLOR-NIH REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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: 17380 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 O ASN A 267 H GLY A 271 1.32 REMARK 500 O TYR A 146 H GLY A 148 1.40 REMARK 500 O LYS A 266 HD21 ASN A 267 1.50 REMARK 500 O ASP A 264 H ASN A 267 1.60 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 1 ILE A 227 CA - CB - CG2 ANGL. DEV. = 13.1 DEGREES REMARK 500 3 ILE A 227 CB - CA - C ANGL. DEV. = 12.5 DEGREES REMARK 500 6 ILE A 227 CG1 - CB - CG2 ANGL. DEV. = 14.2 DEGREES REMARK 500 9 ILE A 227 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 10 ILE A 227 CG1 - CB - CG2 ANGL. DEV. = 13.3 DEGREES REMARK 500 12 ILE A 227 CG1 - CB - CG2 ANGL. DEV. = 13.5 DEGREES REMARK 500 19 ILE A 227 CA - CB - CG1 ANGL. DEV. = 12.3 DEGREES REMARK 500 20 ILE A 227 CB - CA - C ANGL. DEV. = -13.0 DEGREES REMARK 500 20 ILE A 227 CA - CB - CG1 ANGL. DEV. = 14.4 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 1 VAL A 3 69.46 29.23 REMARK 500 1 PRO A 5 -90.70 -67.01 REMARK 500 1 THR A 6 125.05 96.50 REMARK 500 1 TYR A 22 102.00 56.09 REMARK 500 1 PHE A 24 -138.84 -113.41 REMARK 500 1 GLU A 40 79.63 57.15 REMARK 500 1 ARG A 63 -112.90 79.16 REMARK 500 1 TRP A 64 -166.04 148.29 REMARK 500 1 GLU A 66 -97.41 -46.03 REMARK 500 1 LEU A 69 67.46 -106.05 REMARK 500 1 ASP A 78 0.65 -60.90 REMARK 500 1 ASN A 79 -3.15 85.43 REMARK 500 1 ALA A 92 -41.31 176.64 REMARK 500 1 ARG A 93 -80.17 -76.76 REMARK 500 1 ASN A 106 93.49 -36.44 REMARK 500 1 THR A 107 45.84 34.13 REMARK 500 1 ARG A 120 86.21 -171.49 REMARK 500 1 GLU A 121 118.88 34.59 REMARK 500 1 HIS A 122 -14.60 56.82 REMARK 500 1 GLU A 147 52.42 -46.48 REMARK 500 1 THR A 165 -57.12 -120.28 REMARK 500 1 ASP A 176 120.89 -38.36 REMARK 500 1 GLU A 177 -19.35 59.45 REMARK 500 1 THR A 188 -67.62 -122.33 REMARK 500 1 ASN A 199 -169.61 -168.72 REMARK 500 1 ALA A 212 100.41 -41.93 REMARK 500 1 SER A 241 34.90 88.54 REMARK 500 1 PRO A 253 -15.88 -38.69 REMARK 500 1 ALA A 283 -175.69 47.52 REMARK 500 2 PRO A 5 -166.68 -70.14 REMARK 500 2 TYR A 22 -68.91 147.41 REMARK 500 2 ASN A 37 -166.62 -78.72 REMARK 500 2 THR A 49 36.32 -63.22 REMARK 500 2 GLU A 50 -51.31 -159.59 REMARK 500 2 THR A 52 31.02 74.18 REMARK 500 2 ARG A 63 77.62 -109.47 REMARK 500 2 THR A 65 -7.36 64.08 REMARK 500 2 GLU A 66 -81.02 -72.46 REMARK 500 2 ASN A 79 0.78 99.91 REMARK 500 2 LEU A 91 40.32 -148.96 REMARK 500 2 ALA A 92 -0.24 73.16 REMARK 500 2 PRO A 105 -129.42 -37.90 REMARK 500 2 LYS A 109 -112.15 -51.77 REMARK 500 2 ARG A 120 109.49 177.18 REMARK 500 2 GLU A 121 102.76 44.41 REMARK 500 2 HIS A 122 1.90 44.13 REMARK 500 2 TYR A 146 76.34 -150.30 REMARK 500 2 THR A 165 -58.40 -132.61 REMARK 500 2 GLU A 177 -13.07 57.91 REMARK 500 2 THR A 188 -71.38 -112.91 REMARK 500 REMARK 500 THIS ENTRY HAS 539 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30065 RELATED DB: BMRB DBREF 5JDP A 2 283 UNP P21796 VDAC1_HUMAN 2 283 SEQADV 5JDP SER A 1 UNP P21796 EXPRESSION TAG SEQADV 5JDP VAL A 73 UNP P21796 GLU 73 CONFLICT SEQADV 5JDP ARG A 284 UNP P21796 EXPRESSION TAG SEQADV 5JDP SER A 285 UNP P21796 EXPRESSION TAG SEQRES 1 A 285 SER ALA VAL PRO PRO THR TYR ALA ASP LEU GLY LYS SER SEQRES 2 A 285 ALA ARG ASP VAL PHE THR LYS GLY TYR GLY PHE GLY LEU SEQRES 3 A 285 ILE LYS LEU ASP LEU LYS THR LYS SER GLU ASN GLY LEU SEQRES 4 A 285 GLU PHE THR SER SER GLY SER ALA ASN THR GLU THR THR SEQRES 5 A 285 LYS VAL THR GLY SER LEU GLU THR LYS TYR ARG TRP THR SEQRES 6 A 285 GLU TYR GLY LEU THR PHE THR VAL LYS TRP ASN THR ASP SEQRES 7 A 285 ASN THR LEU GLY THR GLU ILE THR VAL GLU ASP GLN LEU SEQRES 8 A 285 ALA ARG GLY LEU LYS LEU THR PHE ASP SER SER PHE SER SEQRES 9 A 285 PRO ASN THR GLY LYS LYS ASN ALA LYS ILE LYS THR GLY SEQRES 10 A 285 TYR LYS ARG GLU HIS ILE ASN LEU GLY CYS ASP MET ASP SEQRES 11 A 285 PHE ASP ILE ALA GLY PRO SER ILE ARG GLY ALA LEU VAL SEQRES 12 A 285 LEU GLY TYR GLU GLY TRP LEU ALA GLY TYR GLN MET ASN SEQRES 13 A 285 PHE GLU THR ALA LYS SER ARG VAL THR GLN SER ASN PHE SEQRES 14 A 285 ALA VAL GLY TYR LYS THR ASP GLU PHE GLN LEU HIS THR SEQRES 15 A 285 ASN VAL ASN ASP GLY THR GLU PHE GLY GLY SER ILE TYR SEQRES 16 A 285 GLN LYS VAL ASN LYS LYS LEU GLU THR ALA VAL ASN LEU SEQRES 17 A 285 ALA TRP THR ALA GLY ASN SER ASN THR ARG PHE GLY ILE SEQRES 18 A 285 ALA ALA LYS TYR GLN ILE ASP PRO ASP ALA CYS PHE SER SEQRES 19 A 285 ALA LYS VAL ASN ASN SER SER LEU ILE GLY LEU GLY TYR SEQRES 20 A 285 THR GLN THR LEU LYS PRO GLY ILE LYS LEU THR LEU SER SEQRES 21 A 285 ALA LEU LEU ASP GLY LYS ASN VAL ASN ALA GLY GLY HIS SEQRES 22 A 285 LYS LEU GLY LEU GLY LEU GLU PHE GLN ALA ARG SER HELIX 1 AA1 GLY A 11 LYS A 20 1 10 HELIX 2 AA2 PRO A 105 GLY A 108 5 4 SHEET 1 AA120 LEU A 26 THR A 33 0 SHEET 2 AA120 PHE A 41 ASN A 48 -1 O GLY A 45 N LEU A 29 SHEET 3 AA120 VAL A 54 ARG A 63 -1 O GLU A 59 N THR A 42 SHEET 4 AA120 LEU A 69 TRP A 75 -1 O VAL A 73 N THR A 60 SHEET 5 AA120 LEU A 81 GLU A 88 -1 O GLY A 82 N LYS A 74 SHEET 6 AA120 GLY A 94 SER A 104 -1 O SER A 101 N THR A 83 SHEET 7 AA120 LYS A 109 ARG A 120 -1 O LYS A 113 N ASP A 100 SHEET 8 AA120 ILE A 123 ASP A 130 -1 O LEU A 125 N TYR A 118 SHEET 9 AA120 SER A 137 TYR A 146 -1 O ARG A 139 N ASP A 128 SHEET 10 AA120 TRP A 149 GLU A 158 -1 O ALA A 151 N LEU A 144 SHEET 11 AA120 ARG A 163 THR A 175 -1 O ALA A 170 N GLY A 152 SHEET 12 AA120 PHE A 178 ASN A 185 -1 O PHE A 178 N THR A 175 SHEET 13 AA120 GLU A 189 LYS A 197 -1 O TYR A 195 N GLN A 179 SHEET 14 AA120 LEU A 202 THR A 211 -1 O THR A 204 N GLN A 196 SHEET 15 AA120 ARG A 218 ASP A 228 -1 O ALA A 222 N ALA A 205 SHEET 16 AA120 ALA A 231 ASN A 238 -1 O PHE A 233 N TYR A 225 SHEET 17 AA120 LEU A 242 LEU A 251 -1 O GLY A 246 N SER A 234 SHEET 18 AA120 ILE A 255 ASP A 264 -1 O ILE A 255 N LEU A 251 SHEET 19 AA120 LYS A 274 GLN A 282 -1 O GLU A 280 N LYS A 256 SHEET 20 AA120 LEU A 26 THR A 33 1 N LYS A 28 O LEU A 277 CISPEP 1 GLY A 135 PRO A 136 1 -1.14 CISPEP 2 GLY A 135 PRO A 136 2 0.00 CISPEP 3 GLY A 135 PRO A 136 3 -0.41 CISPEP 4 GLY A 135 PRO A 136 4 -0.44 CISPEP 5 GLY A 135 PRO A 136 5 -0.05 CISPEP 6 GLY A 135 PRO A 136 6 0.26 CISPEP 7 GLY A 135 PRO A 136 7 0.10 CISPEP 8 GLY A 135 PRO A 136 8 0.05 CISPEP 9 GLY A 135 PRO A 136 9 0.27 CISPEP 10 GLY A 135 PRO A 136 10 -1.63 CISPEP 11 GLY A 135 PRO A 136 11 0.07 CISPEP 12 GLY A 135 PRO A 136 12 0.02 CISPEP 13 GLY A 135 PRO A 136 13 -1.33 CISPEP 14 GLY A 135 PRO A 136 14 0.03 CISPEP 15 GLY A 135 PRO A 136 15 -0.28 CISPEP 16 GLY A 135 PRO A 136 16 -0.43 CISPEP 17 GLY A 135 PRO A 136 17 -0.43 CISPEP 18 GLY A 135 PRO A 136 18 -0.21 CISPEP 19 GLY A 135 PRO A 136 19 -4.26 CISPEP 20 GLY A 135 PRO A 136 20 -0.40 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