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- PDB-5hdf: Hydrolase SeMet-StnA -

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Basic information

Entry
Database: PDB / ID: 5hdf
TitleHydrolase SeMet-StnA
ComponentsHydrolase
KeywordsHYDROLASE
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Hydrolase
Function and homology information
Biological speciesStreptomyces flocculus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsQian, T.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
Authors: Qian, T. / Wo, J. / Zhang, Y. / Song, Q. / Feng, G. / Luo, R. / Lin, S. / Wu, G. / Chen, H.F.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hydrolase
A: Hydrolase
C: Hydrolase
D: Hydrolase


Theoretical massNumber of molelcules
Total (without water)165,5004
Polymers165,5004
Non-polymers00
Water93752
1
B: Hydrolase


Theoretical massNumber of molelcules
Total (without water)41,3751
Polymers41,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hydrolase


Theoretical massNumber of molelcules
Total (without water)41,3751
Polymers41,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hydrolase


Theoretical massNumber of molelcules
Total (without water)41,3751
Polymers41,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hydrolase


Theoretical massNumber of molelcules
Total (without water)41,3751
Polymers41,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.420, 81.970, 118.693
Angle α, β, γ (deg.)90.00, 126.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISBA61 - 37461 - 374
21HISHISAB61 - 37461 - 374
12GLYGLYBA61 - 37561 - 375
22GLYGLYCC61 - 37561 - 375
13GLYGLYBA61 - 37561 - 375
23GLYGLYDD61 - 37561 - 375
14HISHISAB61 - 37461 - 374
24HISHISCC61 - 37461 - 374
15HISHISAB61 - 37461 - 374
25HISHISDD61 - 37461 - 374
16LEULEUCC61 - 37661 - 376
26LEULEUDD61 - 37661 - 376

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Hydrolase


Mass: 41374.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces flocculus (bacteria) / Gene: stnA / Production host: Escherichia coli (E. coli) / References: UniProt: L7PIJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% 2-propanol, 0.1 M Sodium citrate pH 5.0,12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9819 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9819 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. obs: 37623 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.55
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.985 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21957 1870 5 %RANDOM
Rwork0.19228 ---
obs0.19366 35537 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.855 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å20.22 Å2
2--4.49 Å2-0 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9594 0 0 52 9646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199837
X-RAY DIFFRACTIONr_bond_other_d0.0080.028998
X-RAY DIFFRACTIONr_angle_refined_deg1.251.95613431
X-RAY DIFFRACTIONr_angle_other_deg1.22320694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7955.0081264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37523.806444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.337151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5481564
X-RAY DIFFRACTIONr_chiral_restr0.080.21488
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111407
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022251
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_it2.2193.5015064
X-RAY DIFFRACTIONr_mcbond_other2.2153.55063
X-RAY DIFFRACTIONr_mcangle_it3.5275.2476323
X-RAY DIFFRACTIONr_mcangle_other3.5275.2486324
X-RAY DIFFRACTIONr_scbond_it3.5613.8294773
X-RAY DIFFRACTIONr_scbond_other3.5613.8314774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4235.5887109
X-RAY DIFFRACTIONr_long_range_B_refined7.26328.10810628
X-RAY DIFFRACTIONr_long_range_B_other7.26328.11510629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B361120.09
12A361120.09
21B360580.09
22C360580.09
31B358380.09
32D358380.09
41A355780.1
42C355780.1
51A353540.1
52D353540.1
61C361280.09
62D361280.09
LS refinement shellResolution: 2.707→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 115 -
Rwork0.256 2460 -
obs--93.7 %

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