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

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Basic information

Entry
Database: PDB / ID: 21jm
TitleCrystal structure of high-molecular-weight PAH dihydrodiol dehydrogenase PahB from Altererythrobacter sp. H2 in complex with substrate
ComponentsHMW-PAHs dihydrodiol dehydrogenase PahB
KeywordsOXIDOREDUCTASE / Rossmann-like fold / NAD-binding / aromatic compound degradation / dihydrodiol dehydrogenation
Function / homology: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesAltererythrobacter sp. H2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 15, 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)28,8594
Polymers28,0221
Non-polymers8383
Water5,621312
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)115,43816
Polymers112,0874
Non-polymers3,35012
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 area20200 Å2
ΔGint-117 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.837, 79.310, 94.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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
Source: (gene. exp.) Altererythrobacter sp. H2 (bacteria) / 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-A1E25 / (1~{S},2~{R})-cyclohexa-3,5-diene-1,2-diol


Mass: 112.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: ammonium chloride, PEG 3350

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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 PILATUS3 S 6M / 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: 1.35→39.65 Å / Num. obs: 61070 / % possible obs: 98.9 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Χ2: 1.01 / Net I/σ(I): 23.5 / Num. measured all: 782687
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 94.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.548 / Num. measured all: 27341 / Num. unique obs: 2863 / CC1/2: 0.9 / Rpim(I) all: 0.182 / Rrim(I) all: 0.58 / Χ2: 1.02 / Net I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→35.666 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1595 3133 5.13 %
Rwork0.1452 --
obs0.1459 61066 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→35.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 56 312 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082037
X-RAY DIFFRACTIONf_angle_d1.1452764
X-RAY DIFFRACTIONf_dihedral_angle_d10.1091167
X-RAY DIFFRACTIONf_chiral_restr0.089318
X-RAY DIFFRACTIONf_plane_restr0.007352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37110.20781350.2042501X-RAY DIFFRACTION94
1.3711-1.39360.20341610.17822539X-RAY DIFFRACTION97
1.3936-1.41760.20481450.17322603X-RAY DIFFRACTION98
1.4176-1.44340.17911520.16682561X-RAY DIFFRACTION98
1.4434-1.47110.15361300.15832628X-RAY DIFFRACTION98
1.4711-1.50120.14021350.14882578X-RAY DIFFRACTION98
1.5012-1.53380.1571370.14842599X-RAY DIFFRACTION98
1.5338-1.56950.14761360.14182595X-RAY DIFFRACTION98
1.5695-1.60880.15841450.14282599X-RAY DIFFRACTION99
1.6088-1.65220.15011290.13422645X-RAY DIFFRACTION99
1.6522-1.70090.14241240.13652628X-RAY DIFFRACTION99
1.7009-1.75580.14951270.1422658X-RAY DIFFRACTION99
1.7558-1.81850.17641430.14482602X-RAY DIFFRACTION99
1.8185-1.89130.15341460.14412655X-RAY DIFFRACTION99
1.8913-1.97740.16391600.14032613X-RAY DIFFRACTION99
1.9774-2.08160.13631320.1362686X-RAY DIFFRACTION100
2.0816-2.2120.15071530.13572638X-RAY DIFFRACTION100
2.212-2.38280.17161520.14222665X-RAY DIFFRACTION100
2.3828-2.62250.17661180.1512722X-RAY DIFFRACTION100
2.6225-3.00180.16981530.15232694X-RAY DIFFRACTION100
3.0018-3.78130.15111610.13752733X-RAY DIFFRACTION100
3.7813-50.15161590.14482791X-RAY DIFFRACTION99
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)
14.2022-0.2729-0.81453.2868-0.58090.9961-0.0573-0.26120.03290.23270.01820.003-0.0046-0.01430.03120.12280.00760.04620.10960.00520.0514-14.9066-1.2399-20.7118
22.0015-0.11052.2331.6929-0.64618.6210.0394-0.3567-0.00860.4062-0.07770.38640.2344-0.25320.03620.2164-0.01530.12070.20940.00420.1889-24.9871-5.3615-17.5127
32.86310.93842.6160.43410.95482.5910.0103-0.20370.11570.1555-0.0910.160.0755-0.44210.10520.11270.00780.06170.1615-0.00740.1667-26.99415.2835-26.4799
40.52720.0913-0.02091.2820.6191.3831-0.0204-0.00640.00280.03940.00310.12440.0705-0.12640.02570.06210.00010.00680.08410.00770.0827-17.3803-0.6203-39.788
50.87580.44730.0793.8559-0.49660.8592-0.0217-0.0252-0.08880.00680.06270.12060.0969-0.1464-0.02640.0864-0.00050.03990.11390.00110.0506-16.6664-6.5912-34.8736
66.05432.0785-2.95591.2435-1.56352.0693-0.17540.2218-0.116-0.18510.1639-0.17720.0751-0.04420.02240.244-0.05530.05470.1717-0.01690.2211-10.8374-22.6877-35.6632
70.6909-0.11120.10783.55080.33280.5776-0.0038-0.0461-0.03030.0369-0.014-0.04180.050.02060.00440.06480.00440.00470.07780.00760.0551-2.3245-5.1433-31.3741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 175 )
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 205 )
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 219 )
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 264 )

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