PDB Short entry for 5LM1 HEADER HYDROLASE 28-JUL-16 5LM1 TITLE CRYSTAL STRUCTURE OF HD-PTP PHOSPHATASE IN COMPLEX WITH UBAP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIS DOMAIN-CONTAINING PROTEIN TYROSINE PHOSPHATASE,HD-PTP, COMPND 5 PROTEIN TYROSINE PHOSPHATASE TD14,PTP-TD14; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBAP-1; COMPND 10 CHAIN: B; COMPND 11 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: PTPN23, KIAA1471; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS COILED COIL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LEVY REVDAT 4 01-MAY-24 5LM1 1 REMARK REVDAT 3 14-DEC-16 5LM1 1 JRNL REVDAT 2 07-DEC-16 5LM1 1 REVDAT 1 30-NOV-16 5LM1 0 JRNL AUTH D.GAHLOTH,C.LEVY,G.HEAVEN,F.STEFANI,L.WUNDERLEY,P.MOULD, JRNL AUTH 2 M.J.CLIFF,J.BELLA,A.J.FIELDING,P.WOODMAN,L.TABERNERO JRNL TITL STRUCTURAL BASIS FOR SELECTIVE INTERACTION BETWEEN THE ESCRT JRNL TITL 2 REGULATOR HD-PTP AND UBAP1. JRNL REF STRUCTURE V. 24 2115 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27839950 JRNL DOI 10.1016/J.STR.2016.10.006 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.8285 - 4.6324 1.00 2656 134 0.1939 0.2390 REMARK 3 2 4.6324 - 3.6774 1.00 2516 127 0.1893 0.1984 REMARK 3 3 3.6774 - 3.2127 1.00 2478 139 0.2235 0.2690 REMARK 3 4 3.2127 - 2.9190 1.00 2447 153 0.2413 0.3163 REMARK 3 5 2.9190 - 2.7098 1.00 2469 122 0.2716 0.3336 REMARK 3 6 2.7098 - 2.5501 1.00 2484 108 0.3119 0.3907 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 2741 REMARK 3 ANGLE : 0.397 3701 REMARK 3 CHIRALITY : 0.029 435 REMARK 3 PLANARITY : 0.003 482 REMARK 3 DIHEDRAL : 14.565 1726 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LM1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15835 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 44.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: INHOUSE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN, 20% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 2 REMARK 465 MET A 3 REMARK 465 ALA A 4 REMARK 465 ASP A 44 REMARK 465 PRO A 45 REMARK 465 GLU A 46 REMARK 465 THR A 47 REMARK 465 GLN A 119 REMARK 465 ALA A 120 REMARK 465 GLY A 121 REMARK 465 ALA A 122 REMARK 465 LEU A 352 REMARK 465 LYS A 353 REMARK 465 SER B 261 REMARK 465 ASP B 272 REMARK 465 SER B 273 REMARK 465 ASP B 274 REMARK 465 ASP B 275 REMARK 465 SER B 276 REMARK 465 ASN B 277 REMARK 465 GLN B 278 REMARK 465 LYS B 279 REMARK 465 THR B 280 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 LEU A 11 CG CD1 CD2 REMARK 470 VAL A 48 CG1 CG2 REMARK 470 ASN A 50 CG OD1 ND2 REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 ILE A 123 CG1 CG2 CD1 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 SER A 229 OG REMARK 470 LEU A 230 CG CD1 CD2 REMARK 470 THR A 233 OG1 CG2 REMARK 470 HIS A 235 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 239 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 LYS A 247 CG CD CE NZ REMARK 470 ARG A 265 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 282 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 289 CG CD OE1 NE2 REMARK 470 GLU A 331 CG CD OE1 OE2 REMARK 470 GLN A 346 CG CD OE1 NE2 REMARK 470 LEU A 348 CG CD1 CD2 REMARK 470 ASP A 349 CG OD1 OD2 REMARK 470 ARG A 350 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 351 CG CD OE1 OE2 REMARK 470 ASN B 262 CG OD1 ND2 REMARK 470 LYS B 270 CG CD CE NZ 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 GLN A 42 81.99 55.32 REMARK 500 ASN A 50 41.57 -80.59 REMARK 500 THR A 227 -84.32 -72.87 REMARK 500 SER A 229 -57.95 -167.33 REMARK 500 VAL A 231 -50.75 -127.63 REMARK 500 HIS A 235 -110.22 -131.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LM1 A 2 353 UNP Q9H3S7 PTN23_HUMAN 362 713 DBREF 5LM1 B 261 280 PDB 5LM1 5LM1 261 280 SEQRES 1 A 352 PRO MET ALA ALA HIS GLU ALA SER SER LEU TYR SER GLU SEQRES 2 A 352 GLU LYS ALA LYS LEU LEU ARG GLU MET MET ALA LYS ILE SEQRES 3 A 352 GLU ASP LYS ASN GLU VAL LEU ASP GLN PHE MET ASP SER SEQRES 4 A 352 MET GLN LEU ASP PRO GLU THR VAL ASP ASN LEU ASP ALA SEQRES 5 A 352 TYR SER HIS ILE PRO PRO GLN LEU MET GLU LYS CYS ALA SEQRES 6 A 352 ALA LEU SER VAL ARG PRO ASP THR VAL ARG ASN LEU VAL SEQRES 7 A 352 GLN SER MET GLN VAL LEU SER GLY VAL PHE THR ASP VAL SEQRES 8 A 352 GLU ALA SER LEU LYS ASP ILE ARG ASP LEU LEU GLU GLU SEQRES 9 A 352 ASP GLU LEU LEU GLU GLN LYS PHE GLN GLU ALA VAL GLY SEQRES 10 A 352 GLN ALA GLY ALA ILE SER ILE THR SER LYS ALA GLU LEU SEQRES 11 A 352 ALA GLU VAL ARG ARG GLU TRP ALA LYS TYR MET GLU VAL SEQRES 12 A 352 HIS GLU LYS ALA SER PHE THR ASN SER GLU LEU HIS ARG SEQRES 13 A 352 ALA MET ASN LEU HIS VAL GLY ASN LEU ARG LEU LEU SER SEQRES 14 A 352 GLY PRO LEU ASP GLN VAL ARG ALA ALA LEU PRO THR PRO SEQRES 15 A 352 ALA LEU SER PRO GLU ASP LYS ALA VAL LEU GLN ASN LEU SEQRES 16 A 352 LYS ARG ILE LEU ALA LYS VAL GLN GLU MET ARG ASP GLN SEQRES 17 A 352 ARG VAL SER LEU GLU GLN GLN LEU ARG GLU LEU ILE GLN SEQRES 18 A 352 LYS ASP ASP ILE THR ALA SER LEU VAL THR THR ASP HIS SEQRES 19 A 352 SER GLU MET LYS LYS LEU PHE GLU GLU GLN LEU LYS LYS SEQRES 20 A 352 TYR ASP GLN LEU LYS VAL TYR LEU GLU GLN ASN LEU ALA SEQRES 21 A 352 ALA GLN ASP ARG VAL LEU CYS ALA LEU THR GLU ALA ASN SEQRES 22 A 352 VAL GLN TYR ALA ALA VAL ARG ARG VAL LEU SER ASP LEU SEQRES 23 A 352 ASP GLN LYS TRP ASN SER THR LEU GLN THR LEU VAL ALA SEQRES 24 A 352 SER TYR GLU ALA TYR GLU ASP LEU MET LYS LYS SER GLN SEQRES 25 A 352 GLU GLY ARG ASP PHE TYR ALA ASP LEU GLU SER LYS VAL SEQRES 26 A 352 ALA ALA LEU LEU GLU ARG THR GLN SER THR CYS GLN ALA SEQRES 27 A 352 ARG GLU ALA ALA ARG GLN GLN LEU LEU ASP ARG GLU LEU SEQRES 28 A 352 LYS SEQRES 1 B 20 SER ASN ILE LYS SER LEU SER PHE PRO LYS LEU ASP SER SEQRES 2 B 20 ASP ASP SER ASN GLN LYS THR FORMUL 3 HOH *31(H2 O) HELIX 1 AA1 ALA A 5 GLN A 42 1 38 HELIX 2 AA2 ASP A 49 HIS A 56 5 8 HELIX 3 AA3 PRO A 58 LEU A 68 1 11 HELIX 4 AA4 ASP A 73 VAL A 117 1 45 HELIX 5 AA5 SER A 124 GLY A 171 1 48 HELIX 6 AA6 PRO A 172 LEU A 180 1 9 HELIX 7 AA7 SER A 186 ALA A 228 1 43 HELIX 8 AA8 GLU A 237 ARG A 350 1 114 HELIX 9 AA9 ASN B 262 LEU B 266 5 5 CRYST1 48.930 93.270 102.220 90.00 90.00 90.00 P 21 21 21 4 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 0.020437 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009783 0.00000