HEADER HYDROLASE 25-SEP-19 6L03 TITLE STRUCTURE OF PTP-MEG2 AND MUNC18-1-PY145 PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE MEG2,PTPASE MEG2; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: STXBP1-PY145 PEPTIDE; COMPND 9 CHAIN: F; COMPND 10 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: PTPN9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS PTP-MEG2, NSF, VESICLE FUSION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.F.XU,X.CHEN,X.YU,J.P.SUN REVDAT 3 22-NOV-23 6L03 1 REMARK REVDAT 2 13-OCT-21 6L03 1 JRNL REVDAT 1 30-SEP-20 6L03 0 JRNL AUTH Y.F.XU,X.CHEN,Z.YANG,P.XIAO,C.H.LIU,K.S.LI,X.Z.YANG, JRNL AUTH 2 Y.J.WANG,Z.L.ZHU,Z.G.XU,S.ZHANG,C.WANG,Y.C.SONG,W.D.ZHAO, JRNL AUTH 3 C.H.WANG,Z.L.JI,Z.Y.ZHANG,M.CUI,J.P.SUN,X.YU JRNL TITL PTP-MEG2 REGULATES QUANTAL SIZE AND FUSION PORE OPENING JRNL TITL 2 THROUGH TWO DISTINCT STRUCTURAL BASES AND SUBSTRATES. JRNL REF EMBO REP. V. 22 52141 2021 JRNL REFN ESSN 1469-3178 JRNL PMID 33764618 JRNL DOI 10.15252/EMBR.202052141 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 896 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 54.2660 - 3.7865 0.99 2981 163 0.1749 0.1948 REMARK 3 2 3.7865 - 3.0055 1.00 2846 152 0.1991 0.1947 REMARK 3 3 3.0055 - 2.6256 1.00 2817 160 0.2357 0.2670 REMARK 3 4 2.6256 - 2.3855 1.00 2845 138 0.2419 0.2874 REMARK 3 5 2.3855 - 2.2145 1.00 2797 150 0.2576 0.2765 REMARK 3 6 2.2145 - 2.0840 1.00 2813 133 0.2914 0.3639 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.76 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 : 0.008 2494 REMARK 3 ANGLE : 0.968 3376 REMARK 3 CHIRALITY : 0.051 367 REMARK 3 PLANARITY : 0.005 434 REMARK 3 DIHEDRAL : 7.404 2058 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 6L03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18019 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 54.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.19100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.92700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4ICZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 0.2M KSCN, 10% ETHELENE REMARK 280 GLYCOL, 0.1M BIS-TRIS PROPANE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.52400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.03700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.52400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.03700 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: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 GLY A 499 REMARK 465 ALA A 500 REMARK 465 ARG A 501 REMARK 465 SER A 502 REMARK 465 LYS A 503 REMARK 465 GLY A 504 REMARK 465 GLN A 505 REMARK 465 CYS A 506 REMARK 465 SER A 582 REMARK 465 SER A 583 REMARK 465 GLU F 390 REMARK 465 SER F 398 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 313 CG CD OE1 OE2 REMARK 470 ASN A 314 CG OD1 ND2 REMARK 470 VAL A 316 CG1 CG2 REMARK 470 GLU A 329 CD OE1 OE2 REMARK 470 LYS A 394 NZ REMARK 470 GLU A 406 CG CD OE1 OE2 REMARK 470 GLU A 419 CG CD OE1 OE2 REMARK 470 GLU A 453 OE1 OE2 REMARK 470 LYS A 577 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 299 176.12 67.16 REMARK 500 PRO A 315 85.52 -67.68 REMARK 500 THR A 347 -66.89 -95.90 REMARK 500 LYS A 367 23.58 49.82 REMARK 500 THR A 401 65.59 -119.19 REMARK 500 ASP A 421 -2.34 76.32 REMARK 500 MET A 439 -159.76 -122.83 REMARK 500 TYR A 471 -5.12 65.55 REMARK 500 ALA A 515 -123.48 -116.85 REMARK 500 SER A 516 -60.54 -96.10 REMARK 500 ILE A 519 -34.58 -133.85 REMARK 500 ILE A 558 113.33 73.75 REMARK 500 GLN F 392 108.54 84.22 REMARK 500 LEU F 396 19.42 54.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 6L03 A 277 583 UNP P43378 PTN9_HUMAN 277 583 DBREF 6L03 F 390 398 PDB 6L03 6L03 390 398 SEQADV 6L03 ALA A 470 UNP P43378 ASP 470 CONFLICT SEQADV 6L03 ALA A 515 UNP P43378 CYS 515 CONFLICT SEQRES 1 A 307 SER VAL HIS VAL PRO GLY PRO HIS ALA MET THR ILE GLN SEQRES 2 A 307 GLU LEU VAL ASP TYR VAL ASN ALA ARG GLN LYS GLN GLY SEQRES 3 A 307 ILE TYR GLU GLU TYR GLU ASP ILE ARG ARG GLU ASN PRO SEQRES 4 A 307 VAL GLY THR PHE HIS CYS SER MET SER PRO GLY ASN LEU SEQRES 5 A 307 GLU LYS ASN ARG TYR GLY ASP VAL PRO CYS LEU ASP GLN SEQRES 6 A 307 THR ARG VAL LYS LEU THR LYS ARG SER GLY HIS THR GLN SEQRES 7 A 307 THR ASP TYR ILE ASN ALA SER PHE MET ASP GLY TYR LYS SEQRES 8 A 307 GLN LYS ASN ALA TYR ILE GLY THR GLN GLY PRO LEU GLU SEQRES 9 A 307 ASN THR TYR ARG ASP PHE TRP LEU MET VAL TRP GLU GLN SEQRES 10 A 307 LYS VAL LEU VAL ILE VAL MET THR THR ARG PHE GLU GLU SEQRES 11 A 307 GLY GLY ARG ARG LYS CYS GLY GLN TYR TRP PRO LEU GLU SEQRES 12 A 307 LYS ASP SER ARG ILE ARG PHE GLY PHE LEU THR VAL THR SEQRES 13 A 307 ASN LEU GLY VAL GLU ASN MET ASN HIS TYR LYS LYS THR SEQRES 14 A 307 THR LEU GLU ILE HIS ASN THR GLU GLU ARG GLN LYS ARG SEQRES 15 A 307 GLN VAL THR HIS PHE GLN PHE LEU SER TRP PRO ALA TYR SEQRES 16 A 307 GLY VAL PRO SER SER ALA ALA SER LEU ILE ASP PHE LEU SEQRES 17 A 307 ARG VAL VAL ARG ASN GLN GLN SER LEU ALA VAL SER ASN SEQRES 18 A 307 MET GLY ALA ARG SER LYS GLY GLN CYS PRO GLU PRO PRO SEQRES 19 A 307 ILE VAL VAL HIS ALA SER ALA GLY ILE GLY ARG THR GLY SEQRES 20 A 307 THR PHE CYS SER LEU ASP ILE CYS LEU ALA GLN LEU GLU SEQRES 21 A 307 GLU LEU GLY THR LEU ASN VAL PHE GLN THR VAL SER ARG SEQRES 22 A 307 MET ARG THR GLN ARG ALA PHE SER ILE GLN THR PRO GLU SEQRES 23 A 307 GLN TYR TYR PHE CYS TYR LYS ALA ILE LEU GLU PHE ALA SEQRES 24 A 307 GLU LYS GLU GLY MET VAL SER SER SEQRES 1 F 9 GLU SER GLN VAL PTR SER LEU ASP SER HET PTR F 394 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *79(H2 O) HELIX 1 AA1 THR A 287 GLU A 313 1 27 HELIX 2 AA2 PHE A 319 SER A 324 1 6 HELIX 3 AA3 SER A 324 GLU A 329 1 6 HELIX 4 AA4 LEU A 379 ASN A 381 5 3 HELIX 5 AA5 THR A 382 GLN A 393 1 12 HELIX 6 AA6 SER A 476 ASN A 497 1 22 HELIX 7 AA7 ILE A 519 GLY A 539 1 21 HELIX 8 AA8 ASN A 542 ARG A 551 1 10 HELIX 9 AA9 THR A 560 GLU A 578 1 19 SHEET 1 AA1 8 ALA A 360 GLY A 365 0 SHEET 2 AA1 8 GLN A 368 THR A 375 -1 O GLN A 368 N GLY A 365 SHEET 3 AA1 8 ILE A 511 HIS A 514 1 O VAL A 513 N ILE A 373 SHEET 4 AA1 8 VAL A 397 MET A 400 1 N VAL A 399 O VAL A 512 SHEET 5 AA1 8 GLN A 456 PHE A 465 1 O PHE A 465 N MET A 400 SHEET 6 AA1 8 TYR A 442 ASN A 451 -1 N LEU A 447 O VAL A 460 SHEET 7 AA1 8 LEU A 429 ASN A 438 -1 N LEU A 434 O THR A 446 SHEET 8 AA1 8 ARG A 423 PHE A 426 -1 N PHE A 426 O LEU A 429 SHEET 1 AA2 2 GLU A 405 GLU A 406 0 SHEET 2 AA2 2 ARG A 409 ARG A 410 -1 O ARG A 409 N GLU A 406 LINK C VAL F 393 N PTR F 394 1555 1555 1.33 LINK C PTR F 394 N SER F 395 1555 1555 1.33 CISPEP 1 GLY A 282 PRO A 283 0 8.65 CRYST1 71.048 84.074 48.753 90.00 90.00 90.00 P 21 21 2 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 0.014075 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020512 0.00000