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- PDB-9k8r: Structure of Promiscuous short chain dehydrogenase Spm14 in compl... -

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Basic information

Entry
Database: PDB / ID: 9k8r
TitleStructure of Promiscuous short chain dehydrogenase Spm14 in complex with NADPH
ComponentsSpm14
KeywordsBIOSYNTHETIC PROTEIN / Short chain dehydrogenase / coenzyme / NADPH
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesSpiromastix sp. SCSIO F190 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4865
Polymers61,8772
Non-polymers1,6093
Water00
1
A: Spm14
B: Spm14
hetero molecules

A: Spm14
B: Spm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97110
Polymers123,7544
Non-polymers3,2186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area25320 Å2
ΔGint-153 kcal/mol
Surface area35360 Å2
MethodPISA
2
A: Spm14
B: Spm14
hetero molecules

A: Spm14
B: Spm14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97110
Polymers123,7544
Non-polymers3,2186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area16340 Å2
ΔGint-76 kcal/mol
Surface area44350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.285, 123.285, 98.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Spm14


Mass: 30938.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spiromastix sp. SCSIO F190 (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
Has ligand of interestY
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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.2M Sodium thiocyanate, 20%w/v Polyethylene glycol 3,350

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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: Dec 11, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.077→50 Å / Num. obs: 16043 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.055 / Rrim(I) all: 0.175 / Χ2: 0.924 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.1510.21.1017760.7480.9250.3611.1590.893100
3.15-3.21100.9477910.8490.9580.3140.9980.915100
3.21-3.279.90.7018040.8790.9670.2330.7390.927100
3.27-3.349.50.6237980.8990.9730.2120.6580.893100
3.34-3.419.80.4977810.9280.9810.1670.5250.951100
3.41-3.4910.10.458100.940.9850.1480.4740.976100
3.49-3.58100.3667970.9720.9930.1210.3860.957100
3.58-3.689.50.3347960.9630.9910.1140.3530.944100
3.68-3.7810.40.297950.9760.9940.0940.3050.993100
3.78-3.9110.30.2347970.9810.9950.0760.2460.988100
3.91-4.0410.30.2057950.9820.9950.0670.2151.007100
4.04-4.21100.1577900.9890.9970.0520.1650.963100
4.21-4.49.60.1268160.9910.9980.0430.1331.044100
4.4-4.6310.30.1117960.9940.9990.0360.1161.065100
4.63-4.929.70.0978080.9950.9990.0330.1021.019100
4.92-5.310.40.0988060.9930.9980.0320.1030.955100
5.3-5.8310.20.0968110.9930.9980.0310.1010.893100
5.83-6.679.60.088070.9960.9990.0270.0850.808100
6.67-8.49.70.0548220.9980.9990.0180.0580.716100
8.4-508.90.0398470.9980.9990.0130.0420.53599.9

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMS

4bms


Resolution: 3.1→38.504 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 756 4.73 %
Rwork0.1836 --
obs0.1845 15979 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 104 0 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174484
X-RAY DIFFRACTIONf_angle_d1.3436109
X-RAY DIFFRACTIONf_dihedral_angle_d17.7281588
X-RAY DIFFRACTIONf_chiral_restr0.074693
X-RAY DIFFRACTIONf_plane_restr0.008774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.31450.31461200.26623015X-RAY DIFFRACTION99
3.3145-3.64780.25121520.22183036X-RAY DIFFRACTION100
3.6478-4.17510.21061360.18953049X-RAY DIFFRACTION100
4.1751-5.2580.16921850.15483031X-RAY DIFFRACTION100
5.258-38.5040.1811630.16183092X-RAY DIFFRACTION99

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