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- PDB-21fn: Crystal structure of high-molecular-weight PAH dihydrodiol dehydr... -

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Basic information

Entry
Database: PDB / ID: 21fn
TitleCrystal structure of high-molecular-weight PAH dihydrodiol dehydrogenase PahB from Altererythrobacter sp. H2
ComponentsHMW-PAHs dihydrodiol dehydrogenase PahB
KeywordsOXIDOREDUCTASE / Rossmann-like fold / NAD-binding / aromatic compound degradation / dihydrodiol dehydrogenation
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesAltererythrobacter sp. H2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, D.F. / Han, Q. / Guo, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021YFA0909501 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2026
Title: Structural and functional characterization of dihydrodiol dehydrogenase PahB recognizing high-molecular-weight PAH substrates.
Authors: Han, Q. / Tian, L.L. / Guo, L. / Cui, R. / Liu, Z.S. / Li, D.F.
History
DepositionDec 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HMW-PAHs dihydrodiol dehydrogenase PahB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8094
Polymers28,0221
Non-polymers7883
Water4,882271
1
A: HMW-PAHs dihydrodiol dehydrogenase PahB
hetero molecules

A: HMW-PAHs dihydrodiol dehydrogenase PahB
hetero molecules

A: HMW-PAHs dihydrodiol dehydrogenase PahB
hetero molecules

A: HMW-PAHs dihydrodiol dehydrogenase PahB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,23716
Polymers112,0874
Non-polymers3,15012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area21650 Å2
ΔGint-92 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 79.353, 94.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-604-

HOH

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Components

#1: Protein HMW-PAHs dihydrodiol dehydrogenase PahB


Mass: 28021.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: reference WP_324260481.1, N-terminal is His-tag (MGSSHHHHHHSSGLVPRGSH)
Source: (gene. exp.) Altererythrobacter sp. H2 (bacteria) / Gene: pahB / Plasmid: pET-28a(+) / Details (production host): N-terminal His6-tag, T7 promoter / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MgCl2, HEPES pH 7.5, PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→47.47 Å / Num. obs: 37495 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Χ2: 1.01 / Net I/σ(I): 19.4 / Num. measured all: 488040
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.809 / Num. measured all: 22809 / Num. unique obs: 1837 / CC1/2: 0.883 / Rpim(I) all: 0.237 / Rrim(I) all: 0.843 / Χ2: 1.02 / Net I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→32.859 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.168 1900 5.07 %
Rwork0.1494 --
obs0.1504 37490 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 52 271 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082027
X-RAY DIFFRACTIONf_angle_d1.0952750
X-RAY DIFFRACTIONf_dihedral_angle_d8.6581190
X-RAY DIFFRACTIONf_chiral_restr0.067315
X-RAY DIFFRACTIONf_plane_restr0.007352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.18631200.18152553X-RAY DIFFRACTION100
1.64-1.68440.21571320.17932504X-RAY DIFFRACTION100
1.6844-1.73390.22861370.17562502X-RAY DIFFRACTION100
1.7339-1.78990.19841330.17812504X-RAY DIFFRACTION100
1.7899-1.85390.18991520.1642514X-RAY DIFFRACTION100
1.8539-1.92810.18731430.15922487X-RAY DIFFRACTION100
1.9281-2.01580.16791470.16252530X-RAY DIFFRACTION100
2.0158-2.12210.20041480.15742513X-RAY DIFFRACTION100
2.1221-2.2550.181150.14922552X-RAY DIFFRACTION100
2.255-2.42910.18031400.14982526X-RAY DIFFRACTION100
2.4291-2.67340.15791130.15722578X-RAY DIFFRACTION100
2.6734-3.060.16641210.15072556X-RAY DIFFRACTION100
3.06-3.85430.15811490.13692584X-RAY DIFFRACTION100
3.8543-40.14791500.13822687X-RAY DIFFRACTION100
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)
17.25561.8054-0.23677.05322.2380.92880.1977-0.64210.09410.91-0.1017-0.11310.2518-0.0872-0.07870.3168-0.00920.06180.25380.00280.1341-13.4451.5694-20.5736
23.6234-0.53220.32381.942-0.01724.3025-0.0397-0.4293-0.09640.401-0.00220.44780.2066-0.47160.02660.3182-0.02510.12990.26090.0150.2318-20.2371-4.1986-19.4976
34.0183-0.07091.4921.12511.24133.88670.0121-0.32170.18880.3013-0.15780.3962-0.0686-0.93030.11820.22560.02820.14010.3506-0.01270.325-27.05555.2518-26.7109
40.8026-0.2251-0.21471.46740.91943.3482-0.0082-0.0131-0.09410.2448-0.03890.25070.4784-0.32290.1050.1577-0.03050.04250.18230.00920.2406-18.859-7.0062-39.5297
55.1297-0.09312.20574.81861.32133.93050.0576-0.0305-0.24810.0258-0.0920.73660.5204-0.98380.04350.1921-0.10230.01950.33770.01330.2892-26.1157-6.5911-46.8704
61.06210.19010.09493.26441.60452.8005-0.0239-0.05920.08180.12550.02430.1376-0.0539-0.1869-0.00310.11750.01960.01840.14210.00690.1482-14.07723.8426-38.245
71.78111.1460.00434.9981-0.5761.8095-0.0342-0.0972-0.11170.1390.03480.35690.2725-0.40540.02080.1866-0.02260.07140.24930.00080.1664-16.5968-6.5644-35.1083
87.3982-2.4776-4.96182.01622.8935.3173-0.26980.22250.2912-0.48940.269-0.18370.4077-0.0782-0.02790.5268-0.1180.120.33530.00650.3943-10.6693-22.8762-35.8379
91.3301-0.5909-0.21996.02010.99051.558-0.0274-0.111-0.07060.20290.0260.00980.14840.0206-0.00010.13210.0023-0.00390.14270.01330.1152-2.3214-5.2068-31.5546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 118 )
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 175 )
7X-RAY DIFFRACTION7chain 'A' and (resid 176 through 205 )
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 219 )
9X-RAY DIFFRACTION9chain 'A' and (resid 220 through 264 )

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