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- PDB-9rkm: Crystal structure of [FeFe]-hydrogenase CbA5H from Clostridium be... -

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Basic information

Entry
Database: PDB / ID: 9rkm
TitleCrystal structure of [FeFe]-hydrogenase CbA5H from Clostridium beijerinckii in Hinact state
Components[FeFe]-hydrogenase
KeywordsOXIDOREDUCTASE / FeFe Hydrogenase Hydrogen Oxygen stability
Function / homology
Function and homology information


ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain ...Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / 4Fe-4S dicluster domain / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Soluble ligand binding domain / SLBB domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Chem-402 / IRON/SULFUR CLUSTER / [FeFe]-hydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsCarr, S.B. / Alogaidi, A. / Morra, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Citation
Journal: To Be Published
Title: The role of accessory domains in oxygen stability of FeFe hydrogenases
Authors: Alogaidi, A. / Carr, S.B. / George, M. / Love, A. / Pordea, A. / Morra, S.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [FeFe]-hydrogenase
B: [FeFe]-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,98421
Polymers143,8152
Non-polymers4,16919
Water10,305572
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-176 kcal/mol
Surface area48340 Å2
Unit cell
Length a, b, c (Å)167.885, 167.885, 125.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 6 through 99 or resid 102...
d_2ens_1(chain "B" and (resid 6 through 27 or resid 31...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSGLUGLUAA6 - 995 - 98
d_12ALAALAGLNGLNAA102 - 290101 - 289
d_13ALAALASERSERAA292 - 411291 - 410
d_14ASPASPVALVALAA413 - 641412 - 640
d_15402402402402AC701
d_16SF4SF4SF4SF4AD702
d_17SF4SF4SF4SF4AE703
d_18SF4SF4SF4SF4AF704
d_19EPEEPEEPEEPEAG705
d_1101PE1PE1PE1PEAH706
d_21LYSLYSGLUGLUBB6 - 275 - 26
d_22GLYGLYGLNGLNBB31 - 29030 - 289
d_23ALAALASERSERBB292 - 411291 - 410
d_24ASPASPVALVALBB413 - 641412 - 640
d_25402402402402BM701
d_26SF4SF4SF4SF4BN702
d_27SF4SF4SF4SF4BO703
d_28SF4SF4SF4SF4BP704
d_29EPEEPEEPEEPEBQ705
d_2101PE1PE1PE1PEBR706

NCS oper: (Code: givenMatrix: (-0.99999989836, 1.88793241432E-5, -0.000450470872811), (5.33956119493E-5, 0.997050653452, -0.0767462806923), (0.000447693360187, -0.076746296945, -0.997050553119)Vector: ...NCS oper: (Code: given
Matrix: (-0.99999989836, 1.88793241432E-5, -0.000450470872811), (5.33956119493E-5, 0.997050653452, -0.0767462806923), (0.000447693360187, -0.076746296945, -0.997050553119)
Vector: -1.0376406049, -2.42142226841, -66.083094845)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein [FeFe]-hydrogenase


Mass: 71907.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta iscR / References: UniProt: A0A1I9RYV3

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Non-polymers , 8 types, 591 molecules

#2: Chemical ChemComp-402 / dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)


Mass: 354.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5Fe2N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: Dark brown rods
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.1 M HEPES pH 7.3 0.2 M MgCl2 34 % (w/v) PEG 400 / PH range: 7.3-7.7 / Temp details: Ambient temperature in anaerobic glove box

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.96→43.66 Å / Num. obs: 128057 / % possible obs: 99.9 % / Redundancy: 54.3 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.031 / Rrim(I) all: 0.229 / Net I/σ(I): 13.3
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 54.4 % / Rmerge(I) obs: 4.796 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 8978 / CC1/2: 0.389 / Rpim(I) all: 0.653 / Rrim(I) all: 4.84 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→43.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2041 1910 1.49 %
Rwork0.1837 126144 -
obs0.184 128054 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.97 Å2
Refinement stepCycle: LAST / Resolution: 1.96→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 154 572 10632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007310259
X-RAY DIFFRACTIONf_angle_d0.892513858
X-RAY DIFFRACTIONf_chiral_restr0.05271535
X-RAY DIFFRACTIONf_plane_restr0.01051756
X-RAY DIFFRACTIONf_dihedral_angle_d18.0413866
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.550168543936 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.3581360.36028845X-RAY DIFFRACTION99.4
2.01-2.060.34721210.34078904X-RAY DIFFRACTION99.7
2.06-2.120.3341530.30578860X-RAY DIFFRACTION99.7
2.12-2.190.27951320.25418924X-RAY DIFFRACTION99.91
2.19-2.270.23841210.22128956X-RAY DIFFRACTION99.89
2.27-2.360.23681220.20748947X-RAY DIFFRACTION99.97
2.36-2.470.19781240.19649002X-RAY DIFFRACTION99.96
2.47-2.60.19051530.19138915X-RAY DIFFRACTION99.96
2.6-2.760.23191310.199006X-RAY DIFFRACTION99.98
2.76-2.980.23031470.18868990X-RAY DIFFRACTION99.99
2.98-3.280.22061450.19539060X-RAY DIFFRACTION99.98
3.28-3.750.17931260.16969089X-RAY DIFFRACTION100
3.75-4.720.15521550.13479159X-RAY DIFFRACTION99.99
4.72-43.660.18321440.15989487X-RAY DIFFRACTION99.64
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)
10.148214635649-0.0990123128666-0.05142109417790.3197137985540.1392370626660.2013447715690.1250730209420.4365204882050.346574159831-0.155330550864-0.134109621747-0.175632465543-0.236861373893-0.529833763164-0.000222126640680.3838875124310.1155752442620.039339692250.6673998166190.0989369832520.4357302260033.24765297605-38.5282811521-66.3206989954
20.269744387419-0.02368019408250.02112066889490.107934690112-0.04153684598250.0711961775894-0.1162046480140.1070296927870.1981289961360.132891278570.172526278320.0577110192942-0.0638247035057-0.358830696721.97207856567E-50.2954343163470.0586483942120.005546488072230.5930041583420.04414184998240.426241668613-6.67018796092-38.1448455291-47.3089927105
30.778457555385-0.2380117855880.08980106339560.4899120513220.1170110050690.842954390396-0.0136805355007-0.0380322497212-0.08569849433340.0325580310556-0.0257493587457-0.003429191452730.113031306259-0.0320749276754.53768159967E-50.2531184950240.009527001707920.02296337442320.325530886090.01903362400170.30387775398224.097357883-56.6038095984-37.5627277216
40.1396317460040.101350916705-0.06924422548590.203435520707-0.08016557907670.2102226318870.0239397349388-0.3184456543310.3058576314570.238652294828-0.05532924847110.218945447523-0.2503134578740.148115852939-4.87524336197E-50.494732946989-0.07393486995520.02304657319260.645339864832-0.0937615213590.46732370903-4.45181248513-35.57238933652.98285419629
50.217213876309-0.02098352166860.08744450934980.1048913028780.02601284247060.1035374904-0.138333462059-0.06992747357810.2214398102850.02585881868090.133069462614-0.103938910149-0.06334849646580.187612789645-3.72918054243E-50.285679036816-0.03848990105750.001863130200140.516498943013-0.02802339700230.4010257946645.70413123492-36.9847421409-15.9311265759
60.857603064065-0.04003434669390.1355799634080.327119572032-0.08978793078450.679707582980.001901110919570.107272550687-0.0689654966374-0.00388154966086-0.01493229700870.0129582790510.07173639399380.1012851435023.14788721118E-60.257419295980.001758419919610.02062691956020.354681936486-0.01664705270.304579544712-25.0772660972-55.9669542928-24.2724898162
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 113 )AA6 - 1131 - 105
22chain 'A' and (resid 114 through 202 )AA114 - 202106 - 194
33chain 'A' and (resid 203 through 641 )AA203 - 641195 - 633
44chain 'B' and (resid 6 through 113 )BH6 - 1131 - 105
55chain 'B' and (resid 114 through 202 )BH114 - 202106 - 194
66chain 'B' and (resid 203 through 641 )BH203 - 641195 - 633

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