HEADER METAL BINDING PROTEIN 06-JAN-16 2NAM TITLE FULL-LENGTH WT SOD1 IN DPC MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUPEROXIDE DISMUTASE 1, HSOD1; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: BL21; SOURCE 6 VARIANT: DE3; SOURCE 7 GENE: SOD1; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-28A KEYWDS SUPEROXIDE DISMUTASE 1, DPC MICELLE, FULL LENGTH SOD1, PHOSPHOLIPID KEYWDS 2 INTERACTION, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR L.LIM,J.SONG REVDAT 2 16-OCT-19 2NAM 1 REMARK CRYST1 REVDAT 1 14-DEC-16 2NAM 0 JRNL AUTH L.LIM,J.SONG JRNL TITL SALS-LINKED WT-SOD1 ADOPTS A HIGHLY SIMILAR HELICAL JRNL TITL 2 CONFORMATION AS FALS-CAUSING L126Z-SOD1 IN A MEMBRANE JRNL TITL 3 ENVIRONMENT JRNL REF BIOCHIM.BIOPHYS.ACTA V.1858 2223 2016 JRNL REFN ISSN 0006-3002 JRNL PMID 27378311 JRNL DOI 10.1016/J.BBAMEM.2016.06.027 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS 4.5.3 REMARK 3 AUTHORS : DAVID VAN DER SPOEL, AND ERIK LINDAHL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FORCEFIELD ENERGY MINIMIZATION USING REMARK 3 AMBER99SB-IDLN REMARK 4 REMARK 4 2NAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000104629. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 4 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20 MM DPC-1, 0.4 MM [U-13C; U REMARK 210 -15N] ENTITY-2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D 1H-15N NOESY; 3D REMARK 210 1H-15N TOCSY; 3D CBCA(CO)NH; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-5 REMARK 465 RES C SSSEQI REMARK 465 MET A -7 REMARK 465 GLY A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 GLN A 153 C GLN A 153 O -0.229 REMARK 500 2 GLN A 153 C GLN A 153 O -0.229 REMARK 500 3 GLN A 153 C GLN A 153 O -0.228 REMARK 500 4 GLN A 153 C GLN A 153 O -0.230 REMARK 500 5 GLN A 153 C GLN A 153 O -0.228 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 2 ARG A 143 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 143 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 4.1 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 PHE A 45 -44.83 -134.11 REMARK 500 1 PHE A 50 -30.31 173.99 REMARK 500 1 ASN A 53 -40.80 -152.61 REMARK 500 1 THR A 54 -71.81 56.86 REMARK 500 1 CYS A 57 -57.25 60.16 REMARK 500 1 THR A 58 -35.21 -169.41 REMARK 500 1 ALA A 60 -32.97 60.34 REMARK 500 1 HIS A 63 -34.00 -171.85 REMARK 500 1 LEU A 67 19.30 -159.54 REMARK 500 1 SER A 68 -56.95 -151.83 REMARK 500 1 ARG A 69 2.36 -64.80 REMARK 500 1 LYS A 75 -36.15 78.10 REMARK 500 1 ASP A 76 30.29 -95.60 REMARK 500 1 GLU A 77 -75.61 -138.68 REMARK 500 1 HIS A 80 -65.61 -122.66 REMARK 500 1 LEU A 84 -67.23 -101.46 REMARK 500 1 ASP A 92 -45.00 -142.28 REMARK 500 1 LYS A 128 -29.66 -144.92 REMARK 500 1 GLU A 132 -34.68 -144.83 REMARK 500 1 THR A 135 -10.06 56.30 REMARK 500 1 ASN A 139 -32.36 179.48 REMARK 500 2 ALA A 4 -61.81 -92.12 REMARK 500 2 LYS A 9 24.46 -146.28 REMARK 500 2 ASP A 11 34.40 -83.32 REMARK 500 2 PHE A 45 -50.75 -128.66 REMARK 500 2 PHE A 50 -27.82 63.05 REMARK 500 2 ASN A 53 -90.32 -121.57 REMARK 500 2 THR A 54 -56.82 -167.03 REMARK 500 2 ALA A 55 -30.98 -146.84 REMARK 500 2 CYS A 57 -49.79 63.72 REMARK 500 2 THR A 58 -30.09 -173.77 REMARK 500 2 ALA A 60 -40.88 61.04 REMARK 500 2 HIS A 63 30.98 -91.11 REMARK 500 2 PHE A 64 90.38 56.00 REMARK 500 2 ARG A 69 16.90 52.35 REMARK 500 2 LYS A 75 -12.24 54.59 REMARK 500 2 GLU A 77 -81.51 -94.25 REMARK 500 2 HIS A 80 5.38 -165.73 REMARK 500 2 ASP A 83 -62.38 -106.74 REMARK 500 2 GLU A 121 5.27 -68.60 REMARK 500 2 ALA A 123 -33.03 -135.34 REMARK 500 2 ASP A 125 -87.36 -132.57 REMARK 500 2 LYS A 128 -28.16 -159.23 REMARK 500 2 SER A 134 -80.65 -142.59 REMARK 500 2 SER A 142 47.30 -78.54 REMARK 500 3 LYS A 3 -52.05 -169.10 REMARK 500 3 VAL A 7 -74.67 -77.02 REMARK 500 3 LEU A 8 5.06 -60.29 REMARK 500 3 LYS A 9 13.83 -142.26 REMARK 500 3 HIS A 48 -62.20 -93.73 REMARK 500 REMARK 500 THIS ENTRY HAS 132 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 71 GLY A 72 3 -149.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25942 RELATED DB: BMRB DBREF 2NAM A 1 153 UNP P00441 SODC_HUMAN 2 154 SEQADV 2NAM MET A -7 UNP P00441 EXPRESSION TAG SEQADV 2NAM GLY A -6 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A -5 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A -4 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A -3 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A -2 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A -1 UNP P00441 EXPRESSION TAG SEQADV 2NAM HIS A 0 UNP P00441 EXPRESSION TAG SEQRES 1 A 161 MET GLY HIS HIS HIS HIS HIS HIS ALA THR LYS ALA VAL SEQRES 2 A 161 CYS VAL LEU LYS GLY ASP GLY PRO VAL GLN GLY ILE ILE SEQRES 3 A 161 ASN PHE GLU GLN LYS GLU SER ASN GLY PRO VAL LYS VAL SEQRES 4 A 161 TRP GLY SER ILE LYS GLY LEU THR GLU GLY LEU HIS GLY SEQRES 5 A 161 PHE HIS VAL HIS GLU PHE GLY ASP ASN THR ALA GLY CYS SEQRES 6 A 161 THR SER ALA GLY PRO HIS PHE ASN PRO LEU SER ARG LYS SEQRES 7 A 161 HIS GLY GLY PRO LYS ASP GLU GLU ARG HIS VAL GLY ASP SEQRES 8 A 161 LEU GLY ASN VAL THR ALA ASP LYS ASP GLY VAL ALA ASP SEQRES 9 A 161 VAL SER ILE GLU ASP SER VAL ILE SER LEU SER GLY ASP SEQRES 10 A 161 HIS CYS ILE ILE GLY ARG THR LEU VAL VAL HIS GLU LYS SEQRES 11 A 161 ALA ASP ASP LEU GLY LYS GLY GLY ASN GLU GLU SER THR SEQRES 12 A 161 LYS THR GLY ASN ALA GLY SER ARG LEU ALA CYS GLY VAL SEQRES 13 A 161 ILE GLY ILE ALA GLN HELIX 1 1 ALA A 4 LYS A 9 1 6 HELIX 2 2 GLN A 15 SER A 25 1 11 HELIX 3 3 GLY A 27 PHE A 45 1 19 HELIX 4 4 LEU A 84 ASP A 92 1 9 HELIX 5 5 ASP A 96 CYS A 111 1 16 HELIX 6 6 ILE A 113 VAL A 118 1 6 HELIX 7 7 VAL A 119 ASP A 124 1 6 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 0.029034 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016180 0.00000 MODEL 1