PDB Short entry for 1GM1 HEADER HYDROLASE 06-SEP-01 1GM1 TITLE SECOND PDZ DOMAIN (PDZ2) OF PTP-BL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TYROSINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ2; COMPND 5 SYNONYM: NONRECEPTOR-TYPE, 13, PROTEIN-TYROSINE PHOSPHATASE RIP, COMPND 6 PHOSPHOPROTEIN PHOSPHATASE, PROTEIN-TYROSINE-PHOSPHATASE, COMPND 7 PHOSPHOTYROSINE PHOSPHATASE, PTPASE, PTP36, BAS-LIKE; COMPND 8 EC: 3.1.3.48; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PDZ, PTP-BL, FAS INTERACTION, LIM INTERACTION, STRUCTURAL PROTEIN, KEYWDS 2 CYTOSKELETON, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR T.WALMA,M.TESSARI,J.AELEN,J.SCHEPENS,W.HENDRIKS,G.W.VUISTER REVDAT 3 28-MAR-18 1GM1 1 SOURCE JRNL REVDAT 2 24-FEB-09 1GM1 1 VERSN REVDAT 1 08-MAR-02 1GM1 0 JRNL AUTH T.WALMA,C.A.SPRONK,M.TESSARI,J.AELEN,J.SCHEPENS,W.HENDRIKS, JRNL AUTH 2 G.W.VUISTER JRNL TITL STRUCTURE, DYNAMICS AND BINDING CHARACTERISTICS OF THE JRNL TITL 2 SECOND PDZ DOMAIN OF PTP-BL. JRNL REF J. MOL. BIOL. V. 316 1101 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11884147 JRNL DOI 10.1006/JMBI.2002.5402 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS WAS USED REMARK 3 IN THE REFINEMENT PROTOCOL. REMARK 4 REMARK 4 1GM1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1290008455. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N NOESY-HSQC; 13C NOESYHSQC; REMARK 210 13C NOESY-TROSY; HNHA; HCACO[N] REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9 REMARK 210 REMARK 210 REMARK: THE ENSEMBLE WAS DETERMINED USING 3D TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY USING SINGLE AND DOUBLE-LABELED PDZ2. 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: 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 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 6 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 8 PHE A 14 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 8 PHE A 14 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 9 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 10 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 18 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 PHE A 14 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 19 PHE A 14 CB - CG - CD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 23 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 23 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 23 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 24 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 24 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 24 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 25 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 25 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 26 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 26 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 27 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 32 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 33 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 33 ARG A 86 NE - CZ - NH1 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 22 63.29 29.64 REMARK 500 1 THR A 35 -139.97 -94.76 REMARK 500 1 LYS A 50 21.33 82.47 REMARK 500 1 ASN A 87 43.16 -88.97 REMARK 500 1 GLN A 100 -62.01 -97.01 REMARK 500 2 ASN A 87 48.58 -88.51 REMARK 500 3 GLU A 17 78.06 -102.55 REMARK 500 3 LEU A 25 -61.59 -100.71 REMARK 500 3 ARG A 38 120.62 78.71 REMARK 500 3 HIS A 39 -69.77 72.47 REMARK 500 3 LYS A 50 26.53 81.74 REMARK 500 3 ASN A 87 48.81 -78.02 REMARK 500 4 ASN A 34 -64.29 -97.88 REMARK 500 4 ARG A 38 67.24 38.75 REMARK 500 4 HIS A 39 -3.21 69.27 REMARK 500 4 ASN A 87 43.06 -81.04 REMARK 500 5 PRO A 10 23.22 -76.20 REMARK 500 5 ASP A 22 52.12 33.34 REMARK 500 5 LEU A 25 -60.24 -101.28 REMARK 500 5 SER A 36 46.09 -83.28 REMARK 500 5 HIS A 39 19.21 56.69 REMARK 500 5 LYS A 50 20.35 82.29 REMARK 500 5 ASN A 87 39.71 -91.60 REMARK 500 6 SER A 36 36.38 -84.12 REMARK 500 6 ASN A 87 46.22 -86.52 REMARK 500 7 PRO A 10 63.84 -62.34 REMARK 500 7 THR A 35 -135.62 -87.57 REMARK 500 7 LYS A 50 16.34 83.01 REMARK 500 7 ASP A 56 -70.28 -58.91 REMARK 500 7 LEU A 73 32.62 -87.15 REMARK 500 7 ASN A 87 49.82 -94.83 REMARK 500 8 PRO A 10 -177.26 -69.82 REMARK 500 8 LEU A 25 -61.37 -106.65 REMARK 500 8 VAL A 37 -128.83 -100.34 REMARK 500 8 HIS A 39 65.43 151.34 REMARK 500 8 LYS A 50 20.16 82.50 REMARK 500 8 LEU A 73 39.32 -92.27 REMARK 500 8 ASN A 87 53.48 -94.39 REMARK 500 9 THR A 21 -149.81 -97.03 REMARK 500 9 HIS A 39 -68.99 -123.98 REMARK 500 9 LYS A 50 21.76 82.07 REMARK 500 9 LEU A 73 35.96 -99.45 REMARK 500 10 LEU A 25 -63.15 -102.84 REMARK 500 10 THR A 35 -155.94 -116.35 REMARK 500 10 ASN A 87 36.63 -95.65 REMARK 500 11 LEU A 25 -60.58 -99.96 REMARK 500 11 ARG A 38 98.02 82.44 REMARK 500 11 HIS A 39 -73.43 66.55 REMARK 500 11 LEU A 73 44.20 -85.48 REMARK 500 12 ARG A 38 104.74 -53.64 REMARK 500 REMARK 500 THIS ENTRY HAS 144 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 ILE A 27 SER A 28 5 149.48 REMARK 500 GLY A 57 ARG A 58 8 146.57 REMARK 500 GLY A 57 ARG A 58 25 147.84 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 4 ARG A 86 0.12 SIDE CHAIN REMARK 500 5 PHE A 14 0.09 SIDE CHAIN REMARK 500 11 ARG A 58 0.11 SIDE CHAIN REMARK 500 13 ARG A 64 0.11 SIDE CHAIN REMARK 500 14 ARG A 38 0.09 SIDE CHAIN REMARK 500 15 ARG A 38 0.09 SIDE CHAIN REMARK 500 15 ARG A 58 0.09 SIDE CHAIN REMARK 500 18 ARG A 58 0.11 SIDE CHAIN REMARK 500 19 ARG A 38 0.08 SIDE CHAIN REMARK 500 20 ARG A 38 0.08 SIDE CHAIN REMARK 500 20 ARG A 86 0.08 SIDE CHAIN REMARK 500 21 ARG A 58 0.13 SIDE CHAIN REMARK 500 22 ARG A 86 0.08 SIDE CHAIN REMARK 500 23 ARG A 38 0.08 SIDE CHAIN REMARK 500 24 ARG A 58 0.11 SIDE CHAIN REMARK 500 27 ARG A 38 0.08 SIDE CHAIN REMARK 500 28 ARG A 58 0.08 SIDE CHAIN REMARK 500 28 ARG A 64 0.09 SIDE CHAIN REMARK 500 29 ARG A 64 0.12 SIDE CHAIN REMARK 500 30 ARG A 58 0.10 SIDE CHAIN REMARK 500 30 ARG A 64 0.09 SIDE CHAIN REMARK 500 33 ARG A 58 0.11 SIDE CHAIN REMARK 500 34 ARG A 38 0.07 SIDE CHAIN REMARK 500 34 ARG A 58 0.11 SIDE CHAIN REMARK 500 35 ARG A 58 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6092 RELATED DB: BMRB DBREF 1GM1 A 9 102 UNP Q64512 Q64512 1351 1444 SEQRES 1 A 94 LYS PRO GLY ASP THR PHE GLU VAL GLU LEU ALA LYS THR SEQRES 2 A 94 ASP GLY SER LEU GLY ILE SER VAL THR GLY GLY VAL ASN SEQRES 3 A 94 THR SER VAL ARG HIS GLY GLY ILE TYR VAL LYS ALA ILE SEQRES 4 A 94 ILE PRO LYS GLY ALA ALA GLU SER ASP GLY ARG ILE HIS SEQRES 5 A 94 LYS GLY ASP ARG VAL LEU ALA VAL ASN GLY VAL SER LEU SEQRES 6 A 94 GLU GLY ALA THR HIS LYS GLN ALA VAL GLU THR LEU ARG SEQRES 7 A 94 ASN THR GLY GLN VAL VAL HIS LEU LEU LEU GLU LYS GLY SEQRES 8 A 94 GLN VAL PRO HELIX 1 1 ALA A 52 ASP A 56 1 5 HELIX 2 2 HIS A 78 ARG A 86 1 9 SHEET 1 AA 5 ASP A 12 ALA A 19 0 SHEET 2 AA 5 VAL A 91 LYS A 98 -1 O VAL A 92 N LEU A 18 SHEET 3 AA 5 ARG A 64 VAL A 68 -1 O ARG A 64 N GLU A 97 SHEET 4 AA 5 ILE A 42 ILE A 47 -1 O ILE A 42 N VAL A 65 SHEET 5 AA 5 ILE A 27 GLY A 31 -1 O SER A 28 N LYS A 45 SHEET 1 AB 4 ASP A 12 ALA A 19 0 SHEET 2 AB 4 VAL A 91 LYS A 98 -1 O VAL A 92 N LEU A 18 SHEET 3 AB 4 ARG A 64 VAL A 68 -1 O ARG A 64 N GLU A 97 SHEET 4 AB 4 VAL A 71 SER A 72 -1 O VAL A 71 N VAL 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