HEADER METAL BINDING PROTEIN 22-JUL-11 2LG7 TITLE NMR STRUCTURE OF THE PROTEIN YP_001302112.1 FROM PARABACTEROIDES TITLE 2 DISTASONIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 24-151; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503 / DSM 20701 / NCTC 11152; SOURCE 5 GENE: BDI_0720; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PSPEEDET KEYWDS APSY SPECTROSCOPY, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, CALCIUM-BINDING PROTEIN, METAL BINDING PROTEIN, PSI- KEYWDS 3 BIOLOGY EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.SERRANO,B.MOHANTY,M.GERALT,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (JCSG) REVDAT 2 14-JUN-23 2LG7 1 REMARK SEQADV REVDAT 1 21-SEP-11 2LG7 0 JRNL AUTH P.SERRANO,B.MOHANTY,M.GERALT,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE PROTEIN YP_001302112.1 FROM JRNL TITL 2 PARABACTEROIDES DISTASONIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, OPALP REMARK 3 AUTHORS : GUNTERT P. (CYANA), LUGINBUHL, GUNTERT, BILLETER REMARK 3 AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LG7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000102353. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.18 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN, 20 MM SODIUM PHOSPHATE, REMARK 210 25 MM SODIUM CHLORIDE, 5 MM REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 5D REMARK 210 APSY CBCACONH; 4D APSY HACANH; REMARK 210 5D APSY HACACONH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, TOPSPIN, UNIO REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 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 17 VAL A 64 CA - CB - CG2 ANGL. DEV. = 11.0 DEGREES REMARK 500 18 VAL A 99 CG1 - CB - CG2 ANGL. DEV. = -10.1 DEGREES REMARK 500 19 VAL A 64 CA - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 20 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ASP A 2 85.66 174.23 REMARK 500 1 SER A 25 2.72 -151.23 REMARK 500 1 GLU A 62 -77.86 -64.87 REMARK 500 1 ILE A 73 -50.08 -133.46 REMARK 500 1 GLU A 85 -164.56 54.05 REMARK 500 1 VAL A 88 -63.86 75.66 REMARK 500 1 VAL A 89 162.77 52.00 REMARK 500 1 ASN A 90 -68.40 -150.28 REMARK 500 1 ASN A 102 76.42 -61.70 REMARK 500 1 VAL A 112 110.48 -163.04 REMARK 500 1 ARG A 114 33.92 -175.26 REMARK 500 1 ASP A 115 84.58 44.21 REMARK 500 1 ASP A 122 -2.49 -146.47 REMARK 500 2 ASP A 2 163.10 75.10 REMARK 500 2 GLU A 5 54.08 -149.64 REMARK 500 2 ARG A 24 6.67 -58.37 REMARK 500 2 ASN A 35 47.48 -72.19 REMARK 500 2 THR A 44 -7.85 -143.15 REMARK 500 2 LEU A 59 49.32 -81.02 REMARK 500 2 GLU A 85 18.45 56.59 REMARK 500 2 ASP A 86 112.72 65.84 REMARK 500 2 VAL A 89 -36.53 -172.49 REMARK 500 2 ASN A 90 163.32 57.57 REMARK 500 2 ASN A 102 88.96 -45.30 REMARK 500 2 SER A 120 69.21 -154.07 REMARK 500 2 ASP A 122 62.68 -171.77 REMARK 500 3 ASP A 2 169.64 75.45 REMARK 500 3 ASP A 4 66.90 -158.31 REMARK 500 3 GLU A 5 71.43 -110.37 REMARK 500 3 ALA A 49 -177.91 -68.48 REMARK 500 3 VAL A 52 62.50 -158.41 REMARK 500 3 ALA A 60 13.86 -57.96 REMARK 500 3 GLU A 62 -80.25 -70.40 REMARK 500 3 GLU A 85 -171.31 54.76 REMARK 500 3 ASP A 86 94.53 51.32 REMARK 500 3 ASN A 90 -61.47 -146.43 REMARK 500 3 ASN A 102 89.20 -48.48 REMARK 500 3 LYS A 108 117.10 -160.37 REMARK 500 3 ASP A 115 25.43 43.60 REMARK 500 3 LYS A 117 42.80 -74.78 REMARK 500 3 ASN A 125 97.42 -176.05 REMARK 500 4 ARG A 24 32.56 -84.48 REMARK 500 4 SER A 25 37.75 -140.75 REMARK 500 4 LEU A 59 2.74 -65.52 REMARK 500 4 GLU A 62 -80.39 -88.56 REMARK 500 4 PHE A 75 63.71 -159.41 REMARK 500 4 VAL A 82 -168.45 -125.22 REMARK 500 4 VAL A 89 83.30 60.92 REMARK 500 4 PRO A 92 85.12 -66.17 REMARK 500 4 ASN A 102 12.80 -45.64 REMARK 500 REMARK 500 THIS ENTRY HAS 219 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 VAL A 30 VAL A 31 1 141.91 REMARK 500 VAL A 31 VAL A 32 1 134.08 REMARK 500 VAL A 30 VAL A 31 2 140.22 REMARK 500 VAL A 31 VAL A 32 2 149.47 REMARK 500 GLY A 1 ASP A 2 3 139.04 REMARK 500 GLY A 1 ASP A 2 4 133.16 REMARK 500 GLY A 1 ASP A 2 5 -141.76 REMARK 500 GLY A 1 ASP A 2 6 -137.23 REMARK 500 GLY A 116 LYS A 117 7 147.64 REMARK 500 GLY A 1 ASP A 2 8 -139.86 REMARK 500 VAL A 30 VAL A 31 8 144.91 REMARK 500 VAL A 31 VAL A 32 8 142.09 REMARK 500 GLY A 1 ASP A 2 10 -114.86 REMARK 500 ASP A 2 ASP A 3 10 -141.40 REMARK 500 VAL A 89 ASN A 90 10 149.97 REMARK 500 VAL A 81 VAL A 82 11 148.40 REMARK 500 GLY A 1 ASP A 2 12 141.44 REMARK 500 GLY A 1 ASP A 2 13 -148.70 REMARK 500 VAL A 30 VAL A 31 14 147.40 REMARK 500 VAL A 31 VAL A 32 14 149.37 REMARK 500 GLY A 1 ASP A 2 16 -138.24 REMARK 500 VAL A 31 VAL A 32 17 141.28 REMARK 500 GLY A 1 ASP A 2 19 122.85 REMARK 500 VAL A 30 VAL A 31 19 149.88 REMARK 500 VAL A 31 VAL A 32 19 144.95 REMARK 500 VAL A 81 VAL A 82 19 149.76 REMARK 500 GLY A 1 ASP A 2 20 -112.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 127 0.10 SIDE CHAIN REMARK 500 1 TYR A 128 0.07 SIDE CHAIN REMARK 500 4 ARG A 114 0.12 SIDE CHAIN REMARK 500 4 TYR A 128 0.10 SIDE CHAIN REMARK 500 5 TYR A 100 0.09 SIDE CHAIN REMARK 500 5 ARG A 114 0.12 SIDE CHAIN REMARK 500 7 TYR A 100 0.07 SIDE CHAIN REMARK 500 8 ARG A 24 0.09 SIDE CHAIN REMARK 500 9 TYR A 13 0.07 SIDE CHAIN REMARK 500 12 TYR A 127 0.08 SIDE CHAIN REMARK 500 13 TYR A 13 0.09 SIDE CHAIN REMARK 500 13 ARG A 24 0.16 SIDE CHAIN REMARK 500 14 TYR A 100 0.09 SIDE CHAIN REMARK 500 14 TYR A 128 0.09 SIDE CHAIN REMARK 500 15 ARG A 24 0.08 SIDE CHAIN REMARK 500 16 TYR A 13 0.07 SIDE CHAIN REMARK 500 17 ARG A 114 0.08 SIDE CHAIN REMARK 500 20 ARG A 24 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17799 RELATED DB: BMRB REMARK 900 RELATED ID: 2LGE RELATED DB: PDB REMARK 900 CALCIUM-BOUND FORM REMARK 900 RELATED ID: 394811 RELATED DB: TARGETDB DBREF 2LG7 A 2 129 UNP A6L9X6 A6L9X6_PARD8 24 151 SEQADV 2LG7 GLY A 1 UNP A6L9X6 EXPRESSION TAG SEQRES 1 A 129 GLY ASP ASP ASP GLU PRO GLY GLY LYS GLY ALA MET TYR SEQRES 2 A 129 GLU VAL THR ILE GLU GLN SER GLY ASP PHE ARG SER PHE SEQRES 3 A 129 ILE LYS SER VAL VAL VAL VAL ALA ASN GLY THR GLN LEU SEQRES 4 A 129 LYS ASP GLY ALA THR GLY GLU SER LEU ALA SER PRO VAL SEQRES 5 A 129 ILE LEU SER ASP GLU GLU LEU ALA VAL GLU LYS VAL THR SEQRES 6 A 129 LEU SER THR THR GLY LYS ALA ILE GLU PHE ALA VAL SER SEQRES 7 A 129 GLY GLY VAL VAL ASP GLY GLU ASP GLY VAL VAL ASN GLU SEQRES 8 A 129 PRO MET GLN TRP VAL VAL THR VAL TYR LYS ASN GLY LYS SEQRES 9 A 129 GLU ILE GLU LYS LYS SER LEU VAL PHE ARG ASP GLY LYS SEQRES 10 A 129 GLU ILE SER THR ASP ASP LEU ASN LEU TYR TYR ASN HELIX 1 1 SER A 55 LEU A 59 5 5 SHEET 1 A 6 SER A 47 LEU A 48 0 SHEET 2 A 6 LEU A 39 LYS A 40 -1 N LEU A 39 O LEU A 48 SHEET 3 A 6 LYS A 63 THR A 68 -1 O SER A 67 N LYS A 40 SHEET 4 A 6 TYR A 13 GLY A 21 -1 N VAL A 15 O LEU A 66 SHEET 5 A 6 MET A 93 LYS A 101 -1 O TYR A 100 N GLU A 14 SHEET 6 A 6 LYS A 104 PHE A 113 -1 O LYS A 109 N VAL A 97 SHEET 1 B 2 ILE A 27 LYS A 28 0 SHEET 2 B 2 VAL A 81 VAL A 82 -1 O VAL A 82 N ILE A 27 SHEET 1 C 2 PHE A 75 ALA A 76 0 SHEET 2 C 2 TYR A 127 TYR A 128 -1 O TYR A 128 N PHE A 75 CISPEP 1 SER A 50 PRO A 51 1 -15.41 CISPEP 2 SER A 50 PRO A 51 2 -4.14 CISPEP 3 SER A 50 PRO A 51 3 14.21 CISPEP 4 SER A 50 PRO A 51 4 -13.80 CISPEP 5 SER A 50 PRO A 51 5 0.92 CISPEP 6 SER A 50 PRO A 51 6 -13.84 CISPEP 7 SER A 50 PRO A 51 7 -7.23 CISPEP 8 SER A 50 PRO A 51 8 -12.15 CISPEP 9 SER A 50 PRO A 51 9 -16.58 CISPEP 10 SER A 50 PRO A 51 10 -7.50 CISPEP 11 SER A 50 PRO A 51 11 -10.94 CISPEP 12 SER A 50 PRO A 51 12 -13.61 CISPEP 13 SER A 50 PRO A 51 13 -4.12 CISPEP 14 SER A 50 PRO A 51 14 -11.31 CISPEP 15 SER A 50 PRO A 51 15 -24.01 CISPEP 16 SER A 50 PRO A 51 16 -14.80 CISPEP 17 SER A 50 PRO A 51 17 -13.74 CISPEP 18 SER A 50 PRO A 51 18 -17.23 CISPEP 19 SER A 50 PRO A 51 19 6.85 CISPEP 20 SER A 50 PRO A 51 20 -0.71 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 MODEL 1