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- PDB-3ttc: Crystal structure of E. coli HypF with ADP and carbamoyl phosphate -

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Basic information

Entry
Database: PDB / ID: 3ttc
TitleCrystal structure of E. coli HypF with ADP and carbamoyl phosphate
ComponentsTranscriptional regulatory protein
KeywordsTRANSFERASE / Zn finger / nucleotide binding / hydrogenase maturation factor
Function / homology
Function and homology information


protein carbamoylation / Ligases; Forming carbon-sulfur bonds / acylphosphatase activity / carboxyl- or carbamoyltransferase activity / ligase activity / double-stranded RNA binding / nucleotide binding / zinc ion binding
Similarity search - Function
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 / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination ...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 / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Carbamoyltransferase HypF / Carbamoyltransferase HypF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsPetkun, S. / Shi, R. / Li, Y. / Cygler, M.
CitationJournal: Structure / Year: 2011
Title: Structure of Hydrogenase Maturation Protein HypF with Reaction Intermediates Shows Two Active Sites.
Authors: Petkun, S. / Shi, R. / Li, Y. / Asinas, A. / Munger, C. / Zhang, L. / Waclawek, M. / Soboh, B. / Sawers, R.G. / Cygler, M.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_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_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_conn.ptnr2_label_seq_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: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2017
Polymers71,1261
Non-polymers1,0756
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.360, 77.913, 200.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulatory protein / HypF


Mass: 71126.211 Da / Num. of mol.: 1 / Fragment: UNP residues 92-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 / Gene: ECs3568, hypf / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7ABC4, UniProt: A0A0H3JHT3*PLUS, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M HEPES, pH 8.5, 20 mM magnesium chloride, 2.5% w/v isopropanol, 10% w/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 4, 2010
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.86→100.24 Å / Num. obs: 62057

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→100.24 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.471 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20243 3124 5.1 %RANDOM
Rwork0.15903 ---
obs0.16122 58450 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.86→100.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4922 0 58 918 5898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9687209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50723.846234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5715786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0731539
X-RAY DIFFRACTIONr_chiral_restr0.1060.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024131
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2718
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.53411
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33325347
X-RAY DIFFRACTIONr_scbond_it2.28732103
X-RAY DIFFRACTIONr_scangle_it3.5554.51862
X-RAY DIFFRACTIONr_rigid_bond_restr2.66735251
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 219 -
Rwork0.168 3962 -
obs--93.72 %
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)
10.21790.0939-0.06420.7268-0.13661.05670.03270.0430.0501-0.1069-0.0117-0.0058-0.13870.0804-0.0210.0298-0.0110.0068-0.01580.0234-0.02823.00150.1949.277
20.3754-0.14570.03780.2877-0.0530.55520.0277-0.0279-0.0062-0.02930.00960.0538-0.03220.0002-0.0373-0.02040.007-0.00630.0017-0.0058-0.018114.07438.58127.431
30.03430.0205-0.0770.1605-0.06240.175-0.0005-0.0091-0.0185-0.01520.00260.0144-0.00760.0072-0.002-0.0260.00360.00250.03520.0115-0.023223.91810.08226.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 187
2X-RAY DIFFRACTION2A188 - 378
3X-RAY DIFFRACTION3A379 - 746

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