PDB Short entry for 2M10 HEADER HYDROLASE 09-NOV-12 2M10 TITLE TRANS FORM OF A PHOTOSWITCHABLE PDZ DOMAIN CROSSLINKED WITH AN TITLE 2 AZOBENZENE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ 2 DOMAIN RESIDUES 1361-1456; COMPND 5 SYNONYM: FAS-ASSOCIATED PROTEIN-TYROSINE PHOSPHATASE 1, FAP-1, PTP- COMPND 6 BAS, PROTEIN-TYROSINE PHOSPHATASE 1E, PTP-E1, HPTPE1, PROTEIN- COMPND 7 TYROSINE PHOSPHATASE PTPL1; COMPND 8 EC: 3.1.3.48; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTPN13, PNP1, PTP1E, PTPL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30A(+) KEYWDS PHOTOSWITCH, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.WALSER REVDAT 5 14-JUN-23 2M10 1 REMARK SEQADV LINK REVDAT 4 07-AUG-13 2M10 1 JRNL REVDAT 3 24-JUL-13 2M10 1 JRNL REVDAT 2 17-JUL-13 2M10 1 JRNL REVDAT 1 03-JUL-13 2M10 0 JRNL AUTH B.BUCHLI,S.A.WALDAUER,R.WALSER,M.L.DONTEN,R.PFISTER, JRNL AUTH 2 N.BLOCHLIGER,S.STEINER,A.CAFLISCH,O.ZERBE,P.HAMM JRNL TITL KINETIC RESPONSE OF A PHOTOPERTURBED ALLOSTERIC PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 11725 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23818626 JRNL DOI 10.1073/PNAS.1306323110 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, X-PLOR NIH 2.32 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M10 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000103072. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM [U-100% 15N] PROTEIN, 50 REMARK 210 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 0.1 MM SODIUM REMARK 210 AZIDE, 4.3 % C12E5, 1.8 % N- REMARK 210 HEXANOL, 90% H2O/10% D2O; 0.75 REMARK 210 MM [U-100% 15N] PROTEIN, 50 MM REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.1 MM SODIUM AZIDE, REMARK 210 8.5 MG/ML PF1 PHAGE, 90% H2O/10% REMARK 210 D2O; 0.75 MM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN, 50 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.1 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HNCACB; 3D HCCH-TOCSY; 3D REMARK 210 C(CO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CARA 1.9.0B3, TALOS REMARK 210 3.80F1 REV 2012.080.14.41, CYANA REMARK 210 3.0, PROCHECKNMR, WHAT IF REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 5 ARG A 58 NE ARG A 58 CZ 0.081 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 ASN A 15 104.86 70.71 REMARK 500 1 ASN A 17 9.68 42.64 REMARK 500 1 THR A 29 -171.36 -49.77 REMARK 500 1 SER A 30 -38.22 -38.56 REMARK 500 1 ARG A 32 -70.28 -41.62 REMARK 500 1 GLN A 44 -3.94 66.51 REMARK 500 1 ASN A 81 48.11 -69.14 REMARK 500 1 PRO A 96 98.89 -68.40 REMARK 500 2 ASN A 15 110.59 68.40 REMARK 500 2 ASN A 17 19.04 43.13 REMARK 500 2 LEU A 19 -143.64 -111.60 REMARK 500 2 VAL A 27 17.15 -68.31 REMARK 500 2 ASN A 28 6.04 85.79 REMARK 500 2 THR A 29 -169.44 -42.39 REMARK 500 2 GLN A 44 -12.10 71.22 REMARK 500 3 ASN A 15 109.19 73.61 REMARK 500 3 ASN A 17 -8.18 53.31 REMARK 500 3 ASN A 28 5.99 85.39 REMARK 500 3 THR A 29 -171.05 -45.41 REMARK 500 3 GLN A 44 -1.36 65.04 REMARK 500 3 PRO A 96 98.66 -67.33 REMARK 500 4 ASN A 15 111.28 67.87 REMARK 500 4 ASN A 17 12.01 43.22 REMARK 500 4 VAL A 27 16.75 -69.82 REMARK 500 4 ASN A 28 12.96 86.64 REMARK 500 4 THR A 29 -170.56 -46.15 REMARK 500 4 SER A 30 -44.02 -29.46 REMARK 500 4 ASN A 81 47.78 -70.48 REMARK 500 5 ASN A 15 107.08 75.03 REMARK 500 5 ASN A 17 -9.99 54.97 REMARK 500 5 LEU A 19 -157.15 -147.96 REMARK 500 5 ASN A 28 6.92 82.55 REMARK 500 5 THR A 29 -170.23 -46.28 REMARK 500 5 GLN A 44 -2.73 69.66 REMARK 500 6 ASN A 15 102.25 74.83 REMARK 500 6 ASN A 17 3.08 45.34 REMARK 500 6 VAL A 27 16.21 -67.71 REMARK 500 6 ASN A 28 5.14 81.32 REMARK 500 6 THR A 29 -170.86 -49.02 REMARK 500 6 ASN A 81 -3.37 -58.85 REMARK 500 6 GLN A 94 57.98 84.13 REMARK 500 6 PRO A 96 -163.56 -73.13 REMARK 500 7 ASN A 15 96.89 71.02 REMARK 500 7 ASN A 17 -8.99 50.29 REMARK 500 7 LEU A 19 -150.75 -87.12 REMARK 500 7 ASN A 28 6.43 85.64 REMARK 500 7 THR A 29 -168.39 -45.89 REMARK 500 7 ASN A 81 53.21 -68.79 REMARK 500 7 LYS A 92 -79.96 34.79 REMARK 500 8 ASN A 15 104.38 72.43 REMARK 500 REMARK 500 THIS ENTRY HAS 147 RAMACHANDRAN OUTLIERS. 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 17 ARG A 80 0.08 SIDE CHAIN REMARK 500 18 ARG A 58 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 33B A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2M0Z RELATED DB: PDB REMARK 900 RELATED ID: 18834 RELATED DB: BMRB DBREF 2M10 A 2 97 UNP Q12923 PTN13_HUMAN 1361 1456 SEQADV 2M10 GLY A 1 UNP Q12923 EXPRESSION TAG SEQADV 2M10 CYS A 22 UNP Q12923 SER 1381 ENGINEERED MUTATION SEQADV 2M10 CYS A 77 UNP Q12923 GLU 1436 ENGINEERED MUTATION SEQRES 1 A 97 GLY PRO LYS PRO GLY ASP ILE PHE GLU VAL GLU LEU ALA SEQRES 2 A 97 LYS ASN ASP ASN SER LEU GLY ILE CYS VAL THR GLY GLY SEQRES 3 A 97 VAL ASN THR SER VAL ARG HIS GLY GLY ILE TYR VAL LYS SEQRES 4 A 97 ALA VAL ILE PRO GLN GLY ALA ALA GLU SER ASP GLY ARG SEQRES 5 A 97 ILE HIS LYS GLY ASP ARG VAL LEU ALA VAL ASN GLY VAL SEQRES 6 A 97 SER LEU GLU GLY ALA THR HIS LYS GLN ALA VAL CYS THR SEQRES 7 A 97 LEU ARG ASN THR GLY GLN VAL VAL HIS LEU LEU LEU GLU SEQRES 8 A 97 LYS GLY GLN SER PRO THR HET 33B A 101 42 HETNAM 33B 3,3'-(E)-DIAZENE-1,2-DIYLBIS{6-[(CHLOROACETYL) HETNAM 2 33B AMINO]BENZENESULFONIC ACID} FORMUL 2 33B C16 H14 CL2 N4 O8 S2 HELIX 1 1 GLY A 45 GLY A 51 1 7 HELIX 2 2 THR A 71 ASN A 81 1 11 SHEET 1 A 5 ILE A 7 ALA A 13 0 SHEET 2 A 5 VAL A 85 GLU A 91 -1 O VAL A 86 N LEU A 12 SHEET 3 A 5 ARG A 58 VAL A 62 -1 N LEU A 60 O LEU A 89 SHEET 4 A 5 ILE A 36 ALA A 40 -1 N ILE A 36 O VAL A 59 SHEET 5 A 5 CYS A 22 GLY A 25 -1 N THR A 24 O TYR A 37 SHEET 1 B 4 ILE A 7 ALA A 13 0 SHEET 2 B 4 VAL A 85 GLU A 91 -1 O VAL A 86 N LEU A 12 SHEET 3 B 4 ARG A 58 VAL A 62 -1 N LEU A 60 O LEU A 89 SHEET 4 B 4 VAL A 65 SER A 66 -1 O VAL A 65 N VAL A 62 LINK SG CYS A 22 C1 33B A 101 1555 1555 1.83 LINK SG CYS A 77 C20 33B A 101 1555 1555 1.82 SITE 1 AC1 8 ILE A 21 CYS A 22 LYS A 39 HIS A 72 SITE 2 AC1 8 LYS A 73 GLN A 74 VAL A 76 CYS A 77 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