10 20 30 40 50 60 70 80 1X3H - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL BINDING PROTEIN 09-MAY-05 1X3H
TITLE SOLUTION STRUCTURE OF THE LIM DOMAIN OF HUMAN LEUPAXIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUPAXIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIM DOMAIN; 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: LPXN; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040809-04; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS LEUPAXIN, PAXILLIN FAMILY, PROTEIN-PROTEIN INTERACTION, LIM KEYWDS 2 DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 4 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, METAL KEYWDS 5 BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR M.YONEYAMA,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 24-FEB-09 1X3H 1 VERSN REVDAT 2 17-JAN-06 1X3H 1 JRNL TITLE REVDAT 1 09-NOV-05 1X3H 0
JRNL AUTH M.YONEYAMA,N.TOCHIO,S.KOSHIBA,M.INOUE,T.KIGAWA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE LIM DOMAIN OF HUMAN JRNL TITL 2 LEUPAXIN JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1X3H COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-05. REMARK 100 THE RCSB ID CODE IS RCSB024331.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.06MM LIM DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL; 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 0.05MM REMARK 210 ZNCL2; 10%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, NMRPIPE REMARK 210 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, TARGET REMARK 210 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 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 LEU A 11 98.51 -45.00 REMARK 500 1 ALA A 12 40.59 -95.07 REMARK 500 1 SER A 15 152.67 -37.00 REMARK 500 1 LEU A 26 -58.13 -132.18 REMARK 500 1 PRO A 39 10.82 -69.77 REMARK 500 1 PHE A 42 90.57 -47.47 REMARK 500 1 ASP A 46 -65.55 -93.23 REMARK 500 1 PHE A 51 40.92 -96.69 REMARK 500 1 SER A 75 93.31 -59.09 REMARK 500 2 PRO A 16 -165.38 -69.72 REMARK 500 2 LEU A 26 -52.50 -128.29 REMARK 500 2 PRO A 39 8.63 -69.75 REMARK 500 2 PHE A 42 90.19 -49.16 REMARK 500 2 ASP A 46 -64.02 -99.90 REMARK 500 2 GLU A 66 -57.31 -28.07 REMARK 500 3 LEU A 11 104.83 -43.44 REMARK 500 3 MET A 13 30.55 -84.42 REMARK 500 3 LEU A 26 -54.59 -129.12 REMARK 500 3 PRO A 39 7.58 -69.74 REMARK 500 3 PHE A 42 91.18 -45.58 REMARK 500 3 ASP A 46 -65.18 -100.31 REMARK 500 3 PHE A 51 41.67 -101.15 REMARK 500 4 ALA A 12 -60.82 -93.55 REMARK 500 4 LEU A 26 -45.17 -130.50 REMARK 500 4 PRO A 39 8.02 -69.81 REMARK 500 4 PHE A 42 99.80 -48.49 REMARK 500 4 ASP A 46 -64.92 -103.77 REMARK 500 4 SER A 55 109.62 -45.07 REMARK 500 4 PHE A 56 173.50 -49.80 REMARK 500 4 GLU A 66 -56.24 -28.48 REMARK 500 4 SER A 75 106.66 -45.34 REMARK 500 4 PRO A 77 94.45 -69.71 REMARK 500 5 SER A 2 44.90 34.21 REMARK 500 5 PRO A 39 7.63 -69.71 REMARK 500 5 PHE A 42 89.42 -47.90 REMARK 500 5 CYS A 44 168.29 -47.68 REMARK 500 5 SER A 55 106.26 -35.75 REMARK 500 6 LEU A 11 96.58 -43.02 REMARK 500 6 SER A 15 152.65 -39.07 REMARK 500 6 LEU A 26 -54.47 -129.88 REMARK 500 6 PRO A 39 8.34 -69.78 REMARK 500 6 PHE A 42 92.90 -47.99 REMARK 500 6 ASP A 46 -64.66 -101.01 REMARK 500 6 GLU A 66 -60.13 -28.00 REMARK 500 6 PRO A 77 6.65 -69.77 REMARK 500 6 SER A 78 147.43 -32.83 REMARK 500 7 PHE A 10 -61.53 -101.15 REMARK 500 7 PHE A 14 38.64 -90.81 REMARK 500 7 PRO A 39 6.81 -69.73 REMARK 500 7 PHE A 42 92.53 -49.85 REMARK 500 7 CYS A 44 164.49 -45.05 REMARK 500 7 ASP A 46 -64.68 -103.39 REMARK 500 7 PHE A 51 43.87 -101.57 REMARK 500 7 THR A 53 36.13 39.18 REMARK 500 7 SER A 55 104.83 -59.81 REMARK 500 7 PHE A 56 177.68 -54.58 REMARK 500 7 SER A 75 107.87 -36.27 REMARK 500 8 ASP A 9 103.31 -37.49 REMARK 500 8 PHE A 10 174.27 -56.15 REMARK 500 8 LEU A 11 105.06 -46.51 REMARK 500 8 MET A 13 42.95 34.53 REMARK 500 8 LEU A 26 -62.82 -104.82 REMARK 500 8 ASN A 28 51.25 34.18 REMARK 500 8 PRO A 39 7.57 -69.75 REMARK 500 8 PHE A 42 90.71 -45.09 REMARK 500 8 ASP A 46 -60.14 -102.65 REMARK 500 8 SER A 50 174.92 -59.23 REMARK 500 8 SER A 52 -54.32 -132.91 REMARK 500 8 GLU A 66 -55.68 -28.50 REMARK 500 8 PRO A 77 0.23 -69.80 REMARK 500 9 SER A 5 107.76 -165.58 REMARK 500 9 LEU A 11 40.20 32.76 REMARK 500 9 LEU A 26 -59.79 -132.58 REMARK 500 9 PRO A 39 9.97 -69.74 REMARK 500 9 PHE A 42 85.91 -51.10 REMARK 500 9 ASP A 46 -64.08 -101.76 REMARK 500 9 GLU A 66 -60.73 -28.52 REMARK 500 9 SER A 79 42.70 -93.75 REMARK 500 10 PHE A 14 -46.13 -134.78 REMARK 500 10 ASN A 22 34.71 72.87 REMARK 500 10 ASN A 28 51.42 36.99 REMARK 500 10 PRO A 39 6.79 -69.77 REMARK 500 10 PHE A 42 87.77 -48.51 REMARK 500 10 ASP A 46 -64.59 -98.53 REMARK 500 10 PHE A 51 28.91 46.62 REMARK 500 10 SER A 52 45.57 34.16 REMARK 500 10 THR A 53 45.88 28.06 REMARK 500 10 GLU A 66 -58.95 -27.69 REMARK 500 10 PRO A 77 93.58 -69.81 REMARK 500 11 SER A 2 135.21 -172.43 REMARK 500 11 SER A 5 113.80 -161.19 REMARK 500 11 LYS A 8 144.09 -170.01 REMARK 500 11 ASP A 9 98.47 -65.51 REMARK 500 11 LEU A 11 108.44 -162.90 REMARK 500 11 ASN A 22 42.42 73.23 REMARK 500 11 PRO A 39 10.03 -69.76 REMARK 500 11 PHE A 42 86.40 -50.90 REMARK 500 11 ASP A 46 -65.16 -100.07 REMARK 500 11 SER A 52 112.48 -39.45 REMARK 500 11 THR A 53 43.00 36.04 REMARK 500 11 SER A 55 129.14 -36.99 REMARK 500 11 GLU A 66 -57.89 -27.78 REMARK 500 11 PRO A 77 11.56 -69.79 REMARK 500 12 SER A 5 118.86 -170.87 REMARK 500 12 LEU A 11 -61.55 -129.55 REMARK 500 12 PRO A 16 -168.76 -69.77 REMARK 500 12 LEU A 26 -56.21 -124.91 REMARK 500 12 ASN A 28 49.24 39.88 REMARK 500 12 PRO A 39 5.67 -69.79 REMARK 500 12 PHE A 42 98.03 -42.05 REMARK 500 12 CYS A 44 164.59 -48.72 REMARK 500 12 ASP A 46 -66.16 -95.58 REMARK 500 12 THR A 53 39.98 35.66 REMARK 500 12 SER A 55 102.70 -38.62 REMARK 500 12 GLU A 66 -56.58 -28.35 REMARK 500 13 SER A 3 134.60 -170.64 REMARK 500 13 SER A 6 140.14 -170.09 REMARK 500 13 LEU A 26 -59.54 -133.22 REMARK 500 13 PRO A 39 9.30 -69.75 REMARK 500 13 PHE A 42 94.73 -42.79 REMARK 500 13 ASP A 46 -61.47 -97.86 REMARK 500 13 GLU A 66 -61.74 -28.51 REMARK 500 13 SER A 78 94.89 -61.70 REMARK 500 14 LEU A 11 98.19 -48.37 REMARK 500 14 PHE A 14 -37.38 -130.95 REMARK 500 14 LEU A 26 -60.79 -129.62 REMARK 500 14 PRO A 39 11.49 -69.74 REMARK 500 14 PHE A 42 91.90 -45.71 REMARK 500 14 CYS A 44 165.23 -47.39 REMARK 500 14 LEU A 67 -70.28 -49.97 REMARK 500 15 SER A 6 119.70 -169.75 REMARK 500 15 LEU A 26 -40.31 -133.14 REMARK 500 15 PRO A 39 10.81 -69.82 REMARK 500 15 PHE A 42 96.87 -48.84 REMARK 500 15 ASP A 46 -63.37 -100.26 REMARK 500 15 SER A 52 -54.22 -120.70 REMARK 500 15 GLU A 66 -61.40 -28.69 REMARK 500 15 SER A 79 42.20 -97.60 REMARK 500 16 SER A 5 122.59 -173.47 REMARK 500 16 SER A 6 139.05 -170.22 REMARK 500 16 LYS A 8 36.92 -97.64 REMARK 500 16 LEU A 11 106.81 -41.73 REMARK 500 16 ALA A 12 42.74 -109.00 REMARK 500 16 PHE A 14 -50.36 -123.16 REMARK 500 16 PRO A 39 9.31 -69.70 REMARK 500 16 PHE A 42 96.77 -42.83 REMARK 500 16 CYS A 44 168.16 -47.54 REMARK 500 16 PHE A 51 74.62 -107.86 REMARK 500 16 GLU A 66 -54.38 -27.82 REMARK 500 16 PRO A 77 6.28 -69.77 REMARK 500 17 ALA A 12 -60.36 -98.34 REMARK 500 17 ASN A 22 35.76 71.29 REMARK 500 17 PRO A 39 11.21 -69.72 REMARK 500 17 PHE A 42 91.56 -45.61 REMARK 500 17 LEU A 67 -70.71 -47.92 REMARK 500 18 SER A 2 108.97 -174.19 REMARK 500 18 ALA A 12 -60.31 -124.97 REMARK 500 18 LEU A 26 -53.07 -125.54 REMARK 500 18 PRO A 39 7.26 -69.80 REMARK 500 18 PHE A 42 92.36 -44.92 REMARK 500 18 ASP A 46 -61.67 -102.43 REMARK 500 18 SER A 52 49.88 -80.28 REMARK 500 18 THR A 53 -56.36 -128.78 REMARK 500 18 GLU A 66 -58.53 -27.52 REMARK 500 18 TYR A 69 -38.39 -32.39 REMARK 500 19 SER A 2 119.85 -169.34 REMARK 500 19 ASP A 9 130.31 -173.21 REMARK 500 19 ALA A 12 108.51 -160.53 REMARK 500 19 PHE A 14 78.34 -101.08 REMARK 500 19 ASN A 22 36.31 74.36 REMARK 500 19 LEU A 26 -46.91 -132.05 REMARK 500 19 PRO A 39 9.33 -69.81 REMARK 500 19 PHE A 42 95.17 -48.65 REMARK 500 19 ASP A 46 -66.22 -91.86 REMARK 500 19 PHE A 56 151.47 -49.11 REMARK 500 19 GLU A 66 -57.51 -27.28 REMARK 500 20 LEU A 11 102.27 -52.47 REMARK 500 20 LEU A 26 -53.98 -131.72 REMARK 500 20 PRO A 39 9.90 -69.78 REMARK 500 20 PHE A 42 96.37 -46.97 REMARK 500 20 ASP A 46 -66.34 -92.35 REMARK 500 20 THR A 53 40.96 -81.50 REMARK 500 20 PRO A 77 -179.28 -69.78 REMARK 500 20 SER A 78 42.32 -93.84 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 120.8 REMARK 620 3 HIS A 38 ND1 97.2 121.1 REMARK 620 4 CYS A 41 SG 119.7 91.9 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 44 SG REMARK 620 2 CYS A 47 SG 94.0 REMARK 620 3 CYS A 65 SG 113.4 93.7 REMARK 620 4 HIS A 68 ND1 117.6 117.5 116.2 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001003110.1 RELATED DB: TARGETDB
DBREF 1X3H A 8 74 UNP O60711 LPXN_HUMAN 260 326
SEQADV 1X3H GLY A 1 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 2 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 3 UNP O60711 CLONING ARTIFACT SEQADV 1X3H GLY A 4 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 5 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 6 UNP O60711 CLONING ARTIFACT SEQADV 1X3H GLY A 7 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 75 UNP O60711 CLONING ARTIFACT SEQADV 1X3H GLY A 76 UNP O60711 CLONING ARTIFACT SEQADV 1X3H PRO A 77 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 78 UNP O60711 CLONING ARTIFACT SEQADV 1X3H SER A 79 UNP O60711 CLONING ARTIFACT SEQADV 1X3H GLY A 80 UNP O60711 CLONING ARTIFACT
SEQRES 1 A 80 GLY SER SER GLY SER SER GLY LYS ASP PHE LEU ALA MET SEQRES 2 A 80 PHE SER PRO LYS CYS GLY GLY CYS ASN ARG PRO VAL LEU SEQRES 3 A 80 GLU ASN TYR LEU SER ALA MET ASP THR VAL TRP HIS PRO SEQRES 4 A 80 GLU CYS PHE VAL CYS GLY ASP CYS PHE THR SER PHE SER SEQRES 5 A 80 THR GLY SER PHE PHE GLU LEU ASP GLY ARG PRO PHE CYS SEQRES 6 A 80 GLU LEU HIS TYR HIS HIS ARG ARG GLY SER GLY PRO SER SEQRES 7 A 80 SER GLY
HET ZN A 201 1 HET ZN A 401 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 CYS A 65 GLY A 74 1 10
SHEET 1 A 2 LEU A 30 ALA A 32 0 SHEET 2 A 2 THR A 35 TRP A 37 -1 O THR A 35 N ALA A 32 SHEET 1 B 2 PHE A 57 GLU A 58 0 SHEET 2 B 2 PRO A 63 PHE A 64 -1 O PHE A 64 N PHE A 57
LINK ZN ZN A 201 SG CYS A 18 1555 1555 2.31 LINK ZN ZN A 201 SG CYS A 21 1555 1555 2.30 LINK ZN ZN A 201 ND1 HIS A 38 1555 1555 2.32 LINK ZN ZN A 201 SG CYS A 41 1555 1555 2.32 LINK ZN ZN A 401 SG CYS A 44 1555 1555 2.33 LINK ZN ZN A 401 SG CYS A 47 1555 1555 2.33 LINK ZN ZN A 401 SG CYS A 65 1555 1555 2.33 LINK ZN ZN A 401 ND1 HIS A 68 1555 1555 2.34
SITE 1 AC1 4 CYS A 18 CYS A 21 HIS A 38 CYS A 41 SITE 1 AC2 4 CYS A 44 CYS A 47 CYS A 65 HIS A 68
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