HEADER HYDROLASE 24-APR-23 8SLT TITLE CRYSTAL STRUCTURE OF HUMAN STEP (PTPN5) AT PHYSIOLOGICAL TEMPERATURE TITLE 2 (310 K) AND AMBIENT PRESSURE (0.1 MPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEURAL-SPECIFIC PROTEIN-TYROSINE PHOSPHATASE,STRIATUM- COMPND 5 ENRICHED PROTEIN-TYROSINE PHOSPHATASE,STEP; COMPND 6 EC: 3.1.3.48; COMPND 7 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: PTPN5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 KEYWDS PTPN5, STEP, PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.EBRAHIM,L.GUERRERO,B.T.RILEY,M.KIM,Q.HUANG,A.D.FINKE,D.A.KEEDY REVDAT 2 27-SEP-23 8SLT 1 COMPND JRNL REMARK ATOM REVDAT 1 21-JUN-23 8SLT 0 JRNL AUTH L.GUERRERO,A.EBRAHIM,B.T.RILEY,M.KIM,Q.HUANG,A.D.FINKE, JRNL AUTH 2 D.A.KEEDY JRNL TITL PUSHED TO EXTREMES: DISTINCT EFFECTS OF HIGH TEMPERATURE VS. JRNL TITL 2 PRESSURE ON THE STRUCTURE OF AN ATYPICAL PHOSPHATASE. JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL PMID 37205580 JRNL DOI 10.1101/2023.05.02.538097 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1358 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 68.6100 - 4.2200 1.00 2650 176 0.1570 0.1598 REMARK 3 2 4.2200 - 3.3500 1.00 2536 138 0.1369 0.1935 REMARK 3 3 3.3500 - 2.9300 1.00 2499 140 0.1583 0.1954 REMARK 3 4 2.9300 - 2.6600 1.00 2498 124 0.1794 0.2207 REMARK 3 5 2.6600 - 2.4700 1.00 2504 126 0.1838 0.2736 REMARK 3 6 2.4700 - 2.3200 1.00 2478 122 0.1940 0.2495 REMARK 3 7 2.3200 - 2.2100 1.00 2460 138 0.2220 0.2538 REMARK 3 8 2.2100 - 2.1100 1.00 2430 134 0.2388 0.2940 REMARK 3 9 2.1100 - 2.0300 1.00 2471 132 0.2858 0.3153 REMARK 3 10 2.0300 - 1.9600 0.99 2426 128 0.3385 0.3676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.00 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 : 0.019 2417 REMARK 3 ANGLE : 1.404 3294 REMARK 3 CHIRALITY : 0.081 357 REMARK 3 PLANARITY : 0.015 429 REMARK 3 DIHEDRAL : 6.244 322 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 8SLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000273987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 310 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : DUAL BOUNCE W/B4C MULTILAYER REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIMPLE V2.6.1 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26353 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 68.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.16970 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 2.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.630 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE V2.6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RECTANGULAR REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 200 MM LI2SO4, 100 MM REMARK 280 BIS-TRIS PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K 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 19.98800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.60500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.24600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.60500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.98800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.24600 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: 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 IN SAME ASYMMETRIC UNIT 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 OE1 GLU A 519 O HOH A 701 2.17 REMARK 500 OD1 ASP A 410 O HOH A 702 2.17 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 ILE A 374 75.68 -117.60 REMARK 500 ASN A 381 10.30 56.78 REMARK 500 LYS A 404 158.24 176.94 REMARK 500 LYS A 439 55.94 -92.33 REMARK 500 CYS A 472 -90.14 -126.62 REMARK 500 CYS A 472 -95.66 -121.53 REMARK 500 SER A 473 -52.02 -120.70 REMARK 500 ILE A 476 -40.16 -136.68 REMARK 500 ILE A 515 96.74 65.13 REMARK 500 ILE A 515 92.72 65.13 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 ARG A 508 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8SLT A 256 537 UNP P54829 PTN5_HUMAN 280 561 SEQADV 8SLT MET A 257 UNP P54829 ALA 281 CONFLICT SEQRES 1 A 282 SER MET SER ARG VAL LEU GLN ALA GLU GLU LEU HIS GLU SEQRES 2 A 282 LYS ALA LEU ASP PRO PHE LEU LEU GLN ALA GLU PHE PHE SEQRES 3 A 282 GLU ILE PRO MET ASN PHE VAL ASP PRO LYS GLU TYR ASP SEQRES 4 A 282 ILE PRO GLY LEU VAL ARG LYS ASN ARG TYR LYS THR ILE SEQRES 5 A 282 LEU PRO ASN PRO HIS SER ARG VAL CYS LEU THR SER PRO SEQRES 6 A 282 ASP PRO ASP ASP PRO LEU SER SER TYR ILE ASN ALA ASN SEQRES 7 A 282 TYR ILE ARG GLY TYR GLY GLY GLU GLU LYS VAL TYR ILE SEQRES 8 A 282 ALA THR GLN GLY PRO ILE VAL SER THR VAL ALA ASP PHE SEQRES 9 A 282 TRP ARG MET VAL TRP GLN GLU HIS THR PRO ILE ILE VAL SEQRES 10 A 282 MET ILE THR ASN ILE GLU GLU MET ASN GLU LYS CYS THR SEQRES 11 A 282 GLU TYR TRP PRO GLU GLU GLN VAL ALA TYR ASP GLY VAL SEQRES 12 A 282 GLU ILE THR VAL GLN LYS VAL ILE HIS THR GLU ASP TYR SEQRES 13 A 282 ARG LEU ARG LEU ILE SER LEU LYS SER GLY THR GLU GLU SEQRES 14 A 282 ARG GLY LEU LYS HIS TYR TRP PHE THR SER TRP PRO ASP SEQRES 15 A 282 GLN LYS THR PRO ASP ARG ALA PRO PRO LEU LEU HIS LEU SEQRES 16 A 282 VAL ARG GLU VAL GLU GLU ALA ALA GLN GLN GLU GLY PRO SEQRES 17 A 282 HIS CYS ALA PRO ILE ILE VAL HIS CYS SER ALA GLY ILE SEQRES 18 A 282 GLY ARG THR GLY CYS PHE ILE ALA THR SER ILE CYS CYS SEQRES 19 A 282 GLN GLN LEU ARG GLN GLU GLY VAL VAL ASP ILE LEU LYS SEQRES 20 A 282 THR THR CYS GLN LEU ARG GLN ASP ARG GLY GLY MET ILE SEQRES 21 A 282 GLN THR CYS GLU GLN TYR GLN PHE VAL HIS HIS VAL MET SEQRES 22 A 282 SER LEU TYR GLU LYS GLN LEU SER HIS HET SO4 A 601 5 HET SO4 A 602 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *69(H2 O) HELIX 1 AA1 GLN A 262 LEU A 271 1 10 HELIX 2 AA2 ASP A 272 PHE A 281 1 10 HELIX 3 AA3 ASP A 289 ASP A 294 5 6 HELIX 4 AA4 GLY A 297 ASN A 302 5 6 HELIX 5 AA5 ASN A 310 HIS A 312 5 3 HELIX 6 AA6 GLY A 337 GLU A 341 5 5 HELIX 7 AA7 ILE A 352 SER A 354 5 3 HELIX 8 AA8 THR A 355 HIS A 367 1 13 HELIX 9 AA9 ASN A 376 MET A 380 5 5 HELIX 10 AB1 THR A 440 ARG A 443 5 4 HELIX 11 AB2 ALA A 444 GLU A 461 1 18 HELIX 12 AB3 ILE A 476 GLY A 496 1 21 HELIX 13 AB4 ASP A 499 ARG A 511 1 13 HELIX 14 AB5 THR A 517 SER A 536 1 20 SHEET 1 AA1 9 ARG A 314 CYS A 316 0 SHEET 2 AA1 9 TYR A 329 ILE A 335 -1 O ALA A 332 N VAL A 315 SHEET 3 AA1 9 TYR A 345 THR A 348 -1 O TYR A 345 N ILE A 335 SHEET 4 AA1 9 ILE A 468 HIS A 471 1 O VAL A 470 N ILE A 346 SHEET 5 AA1 9 ILE A 370 ILE A 374 1 N VAL A 372 O ILE A 469 SHEET 6 AA1 9 GLU A 423 PHE A 432 1 O TYR A 430 N ILE A 371 SHEET 7 AA1 9 TYR A 411 SER A 420 -1 N LEU A 418 O ARG A 425 SHEET 8 AA1 9 VAL A 398 HIS A 407 -1 N GLU A 399 O LYS A 419 SHEET 9 AA1 9 GLN A 392 TYR A 395 -1 N VAL A 393 O ILE A 400 CISPEP 1 SER A 319 PRO A 320 0 4.11 CRYST1 39.976 64.492 137.210 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 0.025015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007288 0.00000