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- PDB-3vti: Crystal structure of HypE-HypF complex -

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Basic information

Entry
Database: PDB / ID: 3vti
TitleCrystal structure of HypE-HypF complex
Components(Hydrogenase maturation ...) x 2
KeywordsTRANSFERASE / carbamoyltransfer / maturation of [NiFe]-hydrogenase / nitrile synthesis / iron / ATP-dependent dehydration
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds / acylphosphatase activity / carboxyl- or carbamoyltransferase activity / ligase activity / protein maturation / double-stranded RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Tetracycline Repressor; domain 2 - #160 / Nucleotidyltransferase; domain 5 - #560 / DHBP synthase - #40 / Translation Initiation Factor IF3 - #120 / Nucleotidyltransferase; domain 5 - #360 / Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / HypF finger / HypF Kae1-like domain ...Tetracycline Repressor; domain 2 - #160 / Nucleotidyltransferase; domain 5 - #560 / DHBP synthase - #40 / Translation Initiation Factor IF3 - #120 / Nucleotidyltransferase; domain 5 - #360 / Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / HypF finger / HypF Kae1-like domain / Carbamoyltransferase, Kae1-like Domain, second subdomain / : / Carbamoyl dehydratase HypE / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / Acylphosphatase-like domain superfamily / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Translation Initiation Factor IF3 / Alpha-Beta Plaits - #100 / Tetracycline Repressor; domain 2 / 60s Ribosomal Protein L30; Chain: A; / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Hydrogenase maturation factor / Carbamoyltransferase
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsShomura, Y. / Higuchi, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for the reaction mechanism of S-carbamoylation of HypE by HypF in the maturation of [NiFe]-hydrogenases
Authors: Shomura, Y. / Higuchi, Y.
History
DepositionMay 30, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrogenase maturation factor
B: Hydrogenase maturation factor
C: Hydrogenase maturation factor
D: Hydrogenase maturation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,90812
Polymers241,4864
Non-polymers4228
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hydrogenase maturation factor
C: Hydrogenase maturation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9546
Polymers120,7432
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-8 kcal/mol
Surface area42530 Å2
MethodPISA
3
B: Hydrogenase maturation factor
D: Hydrogenase maturation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9546
Polymers120,7432
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area42330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.739, 119.101, 174.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Hydrogenase maturation ... , 2 types, 4 molecules ABCD

#1: Protein Hydrogenase maturation factor


Mass: 86867.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HypF, TTE0131 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RDB0, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Protein Hydrogenase maturation factor


Mass: 33875.090 Da / Num. of mol.: 2 / Fragment: N-terminal truncated variant, UNP residues 40-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: HypE, TTE0134 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RDA7

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Non-polymers , 4 types, 401 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M PIPES, 0.48M KCl, 9% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 21, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.56→20 Å / Num. all: 78733 / Num. obs: 78733 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4 / Num. unique all: 3855 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTH (chains A and B), 2RB9 (chains C and D)

3vth

2rb9


Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 25.462 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.879 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25064 3909 5 %RANDOM
Rwork0.20643 ---
obs0.20866 74335 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.492 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2--3.49 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16538 0 8 393 16939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02216862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.97522726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.352094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08324.404772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.661153094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.90115100
X-RAY DIFFRACTIONr_chiral_restr0.0740.22520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.510408
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.745216800
X-RAY DIFFRACTIONr_scbond_it1.01736454
X-RAY DIFFRACTIONr_scangle_it1.7684.55926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.563→2.629 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 219 -
Rwork0.281 4169 -
obs--76.01 %
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)
11.0658-0.29520.14131.5963-0.722.13310.09290.12-0.08760.0381-0.1706-0.0293-0.089-0.09660.07770.07620.01060.03020.0623-0.05460.1333-8.338-39.09336.608
21.31890.03860.52570.70790.19651.4576-0.0587-0.09420.0053-0.05410.1945-0.2429-0.11470.2023-0.13580.1594-0.07270.01370.3119-0.00060.3263-9.029-23.093146.469
32.4519-0.244-0.72121.82040.16012.79910.05120.2089-0.0305-0.1120.103-0.05280.0828-0.0243-0.15410.2335-0.1265-0.03280.12320.0440.10381.636-15.37976.018
41.57290.0546-0.59511.6362-0.1923.6540.0324-0.23790.16580.26820.20320.2433-0.2623-0.3534-0.23560.32290.02120.05950.28390.08180.2279-19.866-9.625103.54
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 751
2X-RAY DIFFRACTION1A801 - 803
3X-RAY DIFFRACTION2B8 - 751
4X-RAY DIFFRACTION2B801 - 803
5X-RAY DIFFRACTION3C38 - 342
6X-RAY DIFFRACTION4D38 - 342

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