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- PDB-9k8q: Structure of Promiscuous Short Chain reductase Spm14 -

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Basic information

Entry
Database: PDB / ID: 9k8q
TitleStructure of Promiscuous Short Chain reductase Spm14
ComponentsSpm14
KeywordsBIOSYNTHETIC PROTEIN / Short chain dehydrogenase
Biological speciesSpiromastix sp. SCSIO F190 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJing, L.Q. / Peng, M. / Chen, Y.Y. / Ju, J.H. / Wu, D.L.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acs Catalysis / Year: 2025
Title: Enzymatic Insights into the Unusual Formation of Benzolactone and Benzopyran in the Biosynthesis of Spiromarmycin
Authors: Chen, Y. / Jing, L. / Peng, M. / Cai, C. / Shi, J. / Ge, W. / Liu, Y. / Shang, Z. / Ma, J. / Wu, D. / Ju, J.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spm14
B: Spm14
C: Spm14


Theoretical massNumber of molelcules
Total (without water)92,8153
Polymers92,8153
Non-polymers00
Water00
1
A: Spm14
B: Spm14
C: Spm14

A: Spm14
B: Spm14
C: Spm14


Theoretical massNumber of molelcules
Total (without water)185,6306
Polymers185,6306
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area15820 Å2
ΔGint-133 kcal/mol
Surface area53310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.689, 122.689, 128.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Spm14


Mass: 30938.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiromastix sp. SCSIO F190 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.1M Succinic acid pH7.0, 0.1M BICINE pH 8.5, 30%v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 12, 2022
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 17303 / % possible obs: 100 % / Redundancy: 19.5 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.03 / Rrim(I) all: 0.131 / Χ2: 0.646 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
3.3-3.3618.51.3258600.840.9560.3161.3630.442
3.36-3.4219.71.3828490.8910.9710.3191.4190.441
3.42-3.4820.31.028410.9030.9740.2321.0470.53
3.48-3.5520.20.938540.9190.9790.2110.9530.443
3.55-3.6320.40.6668470.9580.9890.150.6830.463
3.63-3.7219.60.5458560.9730.9930.1260.560.624
3.72-3.8118.90.4548340.9780.9940.1070.4660.49
3.81-3.9120.60.4098620.9820.9960.0920.4190.619
3.91-4.0320.70.3188580.990.9980.0710.3260.533
4.03-4.1620.40.2558550.9920.9980.0580.2610.558
4.16-4.3120.10.198590.9950.9990.0430.1950.621
4.31-4.4819.20.1628480.9940.9980.0380.1660.722
4.48-4.6819.40.1298670.9960.9990.030.1320.775
4.68-4.9320.30.128750.9960.9990.0270.1240.807
4.93-5.2419.30.1188590.9970.9990.0270.1210.763
5.24-5.6419.20.1038720.9980.9990.0240.1060.751
5.64-6.2120.10.0968750.99810.0220.0990.729
6.21-7.118.30.0728980.99810.0170.0740.819
7.1-8.9418.50.0538860.99910.0120.0550.838
8.94-5015.90.0489480.99910.0120.050.989

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMS

4bms


Resolution: 3.3→42.8 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 872 5.09 %
Rwork0.2434 --
obs0.2448 17144 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5299 0 0 0 5299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055427
X-RAY DIFFRACTIONf_angle_d0.897362
X-RAY DIFFRACTIONf_dihedral_angle_d5.197750
X-RAY DIFFRACTIONf_chiral_restr0.051844
X-RAY DIFFRACTIONf_plane_restr0.01949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50.35631500.30492664X-RAY DIFFRACTION99
3.5-3.770.34091400.26172704X-RAY DIFFRACTION100
3.77-4.150.29981220.26962727X-RAY DIFFRACTION100
4.15-4.750.24321350.21962725X-RAY DIFFRACTION100
4.75-5.980.28271670.25672715X-RAY DIFFRACTION100
5.99-42.80.24481580.2262737X-RAY DIFFRACTION96

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