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- PDB-3zpx: USTILAGO MAYDIS LIPASE UM03410, SHORT FORM WITHOUT FLAP -

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Basic information

Entry
Database: PDB / ID: 3zpx
TitleUSTILAGO MAYDIS LIPASE UM03410, SHORT FORM WITHOUT FLAP
ComponentsLIPASE
KeywordsHYDROLASE / ALPHA BETA HYDROLASE
Function / homology
Function and homology information


434 Repressor (Amino-terminal Domain) - #130 / 434 Repressor (Amino-terminal Domain) / Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / :
Similarity search - Component
Biological speciesUSTILAGO MAYDIS (corn smut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPalm, G.J. / Hinrichs, W.
Citation
#1: Journal: Appl.Microbiol.Biotechnol. / Year: 2012
Title: The Short Form of the Recombinant Cal-A-Type Lipase Um03410 from the Smut Fungus Ustilago Maydis Exhibits an Inherent Trans-Fatty Acid Selectivity.
Authors: Brundiek, H. / Sass, S. / Evitt, A. / Kourist, R. / Bornscheuer, U.T.
History
DepositionMar 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPASE
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1976
Polymers98,7722
Non-polymers4244
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-21.6 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.753, 100.150, 129.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99993, 0.00271, 0.01142), (0.01171, 0.29474, 0.95551), (-0.00077, 0.95557, -0.29475)
Vector: -3.02917, 21.74548, -28.94955)

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Components

#1: Protein LIPASE


Mass: 49386.016 Da / Num. of mol.: 2 / Fragment: SHORT PROTEIN FORM, RESIDUES 152-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) USTILAGO MAYDIS (corn smut) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: Q4P903, triacylglycerol lipase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growpH: 4.5
Details: 30% PEG 8000, 100 MM NAOAC PH 4.5, 200 MM LI2SO4. CRYO SOLUTION: 20% PEG 8000, 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2011 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 47507 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GUU

3guu


Resolution: 1.99→39.57 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.545 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. OVERALL WEIGHTING TERM 0.1. B-FACTOR WEIGHT 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.23469 2373 5 %RANDOM
Rwork0.18283 ---
obs0.18539 45105 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.209 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--1.06 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.99→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5888 0 28 319 6235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196162
X-RAY DIFFRACTIONr_bond_other_d0.0010.025703
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9488404
X-RAY DIFFRACTIONr_angle_other_deg0.7743.00113131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72824.91277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19615921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9091518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021444
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.989→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 149 -
Rwork0.253 2829 -
obs--81.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0249-0.15990.22431.0202-0.39820.85020.01730.1130.02140.1132-0.03590.0285-0.01570.1690.01860.04110.02060.01070.09180.01990.0058-4.99119.25-30.467
20.7732-0.03980.31670.4597-0.081.6097-0.0576-0.0624-0.00040.0449-0.02590.0034-0.2001-0.04010.08340.05970.0054-0.01780.01790.0090.01751.961-2.277-1.983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 395
2X-RAY DIFFRACTION2B14 - 395

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