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- PDB-3vth: Crystal structure of full-length HypF in the phosphate- and nucle... -

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Basic information

Entry
Database: PDB / ID: 3vth
TitleCrystal structure of full-length HypF in the phosphate- and nucleotide-bound form
ComponentsHydrogenase maturation factor
KeywordsTRANSFERASE / carbamoyltransfer / maturation of [NiFe]-hydrogenase / carbamoylphosphate / iron / HypE
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
Similarity search - Function
DHBP synthase - #50 / DHBP synthase - #30 / 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 ...DHBP synthase - #50 / DHBP synthase - #30 / 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 / : / 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. / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / Acylphosphatase-like domain superfamily / Translation Initiation Factor IF3 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / PHOSPHATE ION / Carbamoyltransferase
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,89423
Polymers173,7362
Non-polymers3,15821
Water9,134507
1
A: Hydrogenase maturation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,66814
Polymers86,8681
Non-polymers1,80013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrogenase maturation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2269
Polymers86,8681
Non-polymers1,3588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)232.983, 232.983, 65.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 8 types, 528 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AP2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER


Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N5O9P2
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M imidazole, 1.8M Na/K phosphate, 0.2M NaCl, pH 8.0, 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: Jan 29, 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→20 Å / Num. all: 135176 / Num. obs: 135176 / % possible obs: 98 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 18.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.2 / Num. unique all: 6623 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BSSdata collection
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.191 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23758 6631 5 %RANDOM
Rwork0.20935 ---
obs0.21076 126835 97 %-
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: 46.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.47 Å20 Å2
2---0.95 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11094 0 176 507 11777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211525
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.98615542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68551387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96623.901546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925152085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5361581
X-RAY DIFFRACTIONr_chiral_restr0.0910.21674
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218612
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_it0.5241.56886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.021211117
X-RAY DIFFRACTIONr_scbond_it1.74734639
X-RAY DIFFRACTIONr_scangle_it2.9184.54421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 463 -
Rwork0.257 9031 -
obs--94.46 %
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)
13.1339-0.58222.15411.7404-0.66683.3458-0.1513-0.1240.13170.27090.0658-0.303-0.11340.24450.08550.1521-0.0033-0.09470.0892-0.0110.0699109.777-17.8727.587
20.92460.02360.35432.0098-0.19492.06960.0873-0.1179-0.23670.1222-0.0242-0.11040.3446-0.0525-0.0630.151-0.0359-0.05660.0580.0260.077294.655-29.51614.44
31.37420.8045-0.28891.9085-0.46861.272-0.04420.1366-0.0933-0.28820.08150.03030.262-0.1816-0.03720.1506-0.0366-0.04070.0542-0.00570.013288.291-22.546-7.81
40.6098-0.1742-0.00151.5954-0.48711.8478-0.01560.05020.0156-0.05250.0102-0.1114-0.129-0.16080.00540.07340.0194-0.00520.0389-0.00280.003192.316.437-10.995
53.8592-0.0559-1.99540.68820.4333.1626-0.1826-0.0284-0.85270.5368-0.29140.79450.262-0.8920.4740.7394-0.16570.74870.8012-0.23912.196129.77514.3224.953
62.50660.6301-0.47162.6951-0.00632.74150.0591-0.8159-0.20761.093-0.27310.70880.2446-0.31730.21390.669-0.02280.40740.49050.01120.546348.48224.68616.321
71.6656-0.2410.14422.24660.26520.7483-0.012-0.0534-0.1470.4618-0.00520.2270.0347-0.08990.01720.24630.08040.03790.0741-0.00440.090769.61728.926-2.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 102
2X-RAY DIFFRACTION1A803
3X-RAY DIFFRACTION2A103 - 190
4X-RAY DIFFRACTION2A801 - 802
5X-RAY DIFFRACTION3A191 - 388
6X-RAY DIFFRACTION3A804 - 805
7X-RAY DIFFRACTION4A389 - 755
8X-RAY DIFFRACTION4A806 - 807
9X-RAY DIFFRACTION5B103 - 185
10X-RAY DIFFRACTION5B802
11X-RAY DIFFRACTION6B204 - 388
12X-RAY DIFFRACTION6B804 - 805
13X-RAY DIFFRACTION7B389 - 755
14X-RAY DIFFRACTION7B806 - 807

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