HEADER HYDROLASE 12-MAY-15 4ZRE TITLE CRYSTAL STRUCTURE OF SMG1 F278D MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIP1, SECRETORY LIPASE (FAMILY 3); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-304; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MALASSEZIA GLOBOSA; SOURCE 3 ORGANISM_COMMON: DANDRUFF-ASSOCIATED FUNGUS; SOURCE 4 ORGANISM_TAXID: 425265; SOURCE 5 STRAIN: ATCC MYA-4612 / CBS 7966; SOURCE 6 GENE: MGL_0797; SOURCE 7 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: X33 KEYWDS MONO- AND DIACYLGLYCEROL LIPASE, SECRETORY LIPASE (FAMILY 3), KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.XU,H.XU,S.HOU,J.LIU REVDAT 4 08-NOV-23 4ZRE 1 HETSYN REVDAT 3 29-JUL-20 4ZRE 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 16-DEC-15 4ZRE 1 JRNL REVDAT 1 23-SEP-15 4ZRE 0 JRNL AUTH S.GUO,J.XU,I.V.PAVLIDIS,D.LAN,U.T.BORNSCHEUER,J.LIU,Y.WANG JRNL TITL STRUCTURE OF PRODUCT-BOUND SMG1 LIPASE: ACTIVE SITE GATING JRNL TITL 2 IMPLICATIONS. JRNL REF FEBS J. V. 282 4538 2015 JRNL REFN ISSN 1742-464X JRNL PMID 26365206 JRNL DOI 10.1111/FEBS.13513 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.97 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ZRE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD RUBY CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 18.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3UUE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH5.3, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.61950 REMARK 290 SMTRY3 2 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, 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 SER A 20 REMARK 465 SER A 21 REMARK 465 ILE A 22 REMARK 465 TYR A 23 REMARK 465 ALA A 24 REMARK 465 ARG A 25 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 ASN A 62 116.00 -39.25 REMARK 500 TYR A 79 -74.86 -112.86 REMARK 500 SER A 171 -127.18 63.02 REMARK 500 ASP A 245 134.60 82.43 REMARK 500 GLN A 282 36.76 -97.59 REMARK 500 HIS A 287 3.79 82.00 REMARK 500 ILE A 290 78.88 -108.20 REMARK 500 ALA A 292 -142.73 69.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 793 DISTANCE = 6.45 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZRD RELATED DB: PDB DBREF 4ZRE A 20 304 UNP A8PUY1 A8PUY1_MALGO 20 304 SEQADV 4ZRE ASP A 278 UNP A8PUY1 PHE 278 ENGINEERED MUTATION SEQRES 1 A 285 SER SER ILE TYR ALA ARG GLY ARG GLY GLY SER SER THR SEQRES 2 A 285 ASP GLN PRO VAL ALA ASN PRO TYR ASN THR LYS GLU ILE SEQRES 3 A 285 SER LEU ALA ALA GLY LEU VAL GLN GLN THR TYR CYS ASP SEQRES 4 A 285 SER THR GLU ASN GLY LEU LYS ILE GLY ASP SER GLU LEU SEQRES 5 A 285 LEU TYR THR MET GLY GLU GLY TYR ALA ARG GLN ARG VAL SEQRES 6 A 285 ASN ILE TYR HIS SER PRO SER LEU GLY ILE ALA VAL ALA SEQRES 7 A 285 ILE GLU GLY THR ASN LEU PHE SER LEU ASN SER ASP LEU SEQRES 8 A 285 HIS ASP ALA LYS PHE TRP GLN GLU ASP PRO ASN GLU ARG SEQRES 9 A 285 TYR ILE GLN TYR TYR PRO LYS GLY THR LYS LEU MET HIS SEQRES 10 A 285 GLY PHE GLN GLN ALA TYR ASN ASP LEU MET ASP ASP ILE SEQRES 11 A 285 PHE THR ALA VAL LYS LYS TYR LYS LYS GLU LYS ASN GLU SEQRES 12 A 285 LYS ARG VAL THR VAL ILE GLY HIS SER LEU GLY ALA ALA SEQRES 13 A 285 MET GLY LEU LEU CYS ALA MET ASP ILE GLU LEU ARG MET SEQRES 14 A 285 ASP GLY GLY LEU TYR LYS THR TYR LEU PHE GLY LEU PRO SEQRES 15 A 285 ARG LEU GLY ASN PRO THR PHE ALA SER PHE VAL ASP GLN SEQRES 16 A 285 LYS ILE GLY ASP LYS PHE HIS SER ILE ILE ASN GLY ARG SEQRES 17 A 285 ASP TRP VAL PRO THR VAL PRO PRO ARG ALA LEU GLY TYR SEQRES 18 A 285 GLN HIS PRO SER ASP TYR VAL TRP ILE TYR PRO GLY ASN SEQRES 19 A 285 SER THR SER ALA LYS LEU TYR PRO GLY GLN GLU ASN VAL SEQRES 20 A 285 HIS GLY ILE LEU THR VAL ALA ARG GLU PHE ASN ASP ASP SEQRES 21 A 285 ASP HIS GLN GLY ILE TYR PHE HIS THR GLN ILE GLY ALA SEQRES 22 A 285 VAL MET GLY GLU CYS PRO ALA GLN VAL GLY ALA HIS HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET CL A 504 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM CL CHLORIDE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 3 CL CL 1- FORMUL 4 HOH *193(H2 O) HELIX 1 AA1 ASN A 41 GLN A 54 1 14 HELIX 2 AA2 THR A 55 CYS A 57 5 3 HELIX 3 AA3 ASP A 112 PHE A 115 5 4 HELIX 4 AA4 TYR A 124 TYR A 128 5 5 HELIX 5 AA5 HIS A 136 ASP A 144 1 9 HELIX 6 AA6 LEU A 145 LYS A 160 1 16 HELIX 7 AA7 SER A 171 MET A 188 1 18 HELIX 8 AA8 ASN A 205 GLY A 217 1 13 HELIX 9 AA9 TRP A 229 VAL A 233 5 5 HELIX 10 AB1 PRO A 235 GLY A 239 5 5 HELIX 11 AB2 GLY A 268 VAL A 272 5 5 HELIX 12 AB3 GLY A 291 GLY A 295 5 5 SHEET 1 AA110 VAL A 36 ALA A 37 0 SHEET 2 AA110 ALA A 257 TYR A 260 -1 O LEU A 259 N VAL A 36 SHEET 3 AA110 TYR A 246 ILE A 249 -1 N TYR A 246 O TYR A 260 SHEET 4 AA110 PHE A 220 ASN A 225 1 N ILE A 224 O ILE A 249 SHEET 5 AA110 LYS A 194 PHE A 198 1 N LEU A 197 O HIS A 221 SHEET 6 AA110 VAL A 165 HIS A 170 1 N GLY A 169 O PHE A 198 SHEET 7 AA110 GLY A 93 ILE A 98 1 N VAL A 96 O THR A 166 SHEET 8 AA110 VAL A 84 SER A 89 -1 N ASN A 85 O ALA A 97 SHEET 9 AA110 SER A 69 MET A 75 -1 N LEU A 72 O ILE A 86 SHEET 10 AA110 LYS A 65 ILE A 66 -1 N ILE A 66 O SER A 69 SHEET 1 AA2 2 GLN A 117 GLU A 118 0 SHEET 2 AA2 2 LEU A 134 MET A 135 -1 O LEU A 134 N GLU A 118 SHEET 1 AA3 2 ILE A 284 TYR A 285 0 SHEET 2 AA3 2 THR A 288 GLN A 289 -1 O THR A 288 N TYR A 285 SSBOND 1 CYS A 57 CYS A 297 1555 1555 2.04 LINK ND2 ASN A 253 C1 NAG B 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.42 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.42 CISPEP 1 VAL A 233 PRO A 234 0 -12.10 CISPEP 2 TYR A 250 PRO A 251 0 1.84 CISPEP 3 CYS A 297 PRO A 298 0 -8.32 CRYST1 39.740 73.239 44.919 90.00 108.51 90.00 P 1 21 1 2 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 0.025163 0.000000 0.008423 0.00000 SCALE2 0.000000 0.013654 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023476 0.00000