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- PDB-4q51: Crystal structure of a putative molybdenum cofactor biosynthesis ... -

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Basic information

Entry
Database: PDB / ID: 4q51
TitleCrystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / MoaF
Function / homologyMolybdenum cofactor biosynthesis protein F, N-terminal / MoaF, C-terminal domain / MoaF N-terminal domain / MoaF C-terminal domain / Calycin / metal ion binding / Molybdenum cofactor biosynthesis protein F
Function and homology information
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315
Authors: Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Minasov, G. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
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_label_asym_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.pdbx_leaving_atom_flag / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5594
Polymers62,4792
Non-polymers802
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-44 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.402, 46.163, 77.293
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 31239.619 Da / Num. of mol.: 2 / Fragment: UNP residues 41-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BCAM2002 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: B4EN46
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Calcium Chloride, 0.1 M Tris-HCl, 25 % (w/v) PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2014 / Details: Beryllium Lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 37347 / Num. obs: 37347 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.869 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20871 1869 5 %RANDOM
Rwork0.16028 ---
obs0.16274 35312 95.87 %-
all-35312 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20.01 Å2
2--0.07 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 2 474 4589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194226
X-RAY DIFFRACTIONr_bond_other_d0.0010.023939
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9455766
X-RAY DIFFRACTIONr_angle_other_deg0.84138996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1722.736201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44915612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5091538
X-RAY DIFFRACTIONr_chiral_restr0.1080.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
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_it1.1981.3792119
X-RAY DIFFRACTIONr_mcbond_other1.1971.3782118
X-RAY DIFFRACTIONr_mcangle_it1.8392.0592647
X-RAY DIFFRACTIONr_mcangle_other1.8392.062648
X-RAY DIFFRACTIONr_scbond_it2.1391.6362107
X-RAY DIFFRACTIONr_scbond_other2.1381.6382108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3912.3653120
X-RAY DIFFRACTIONr_long_range_B_refined6.00913.065005
X-RAY DIFFRACTIONr_long_range_B_other5.80112.2954773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 121 -
Rwork0.177 2385 -
obs--87.84 %
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)
11.88020.40551.77121.27260.08741.8307-0.04390.06310.13720.1886-0.03970.2299-0.04060.13820.08360.06220.02320.03790.0657-0.02140.07767.028825.945460.6073
20.9930.2299-0.1610.35260.53151.29380.0507-0.1156-0.08710.0495-0.10970.04150.1105-0.14290.0590.0386-0.01640.00030.05040.00610.0657-4.56624.355353.1136
30.96820.47820.35630.24130.18010.13510.0598-0.0471-0.04490.0293-0.0436-0.01720.0262-0.0344-0.01620.06010.00130.00010.0837-0.00320.01763.914810.666552.6607
41.7696-0.3481.22880.1665-0.04891.24030.0654-0.1441-0.23810.04530.05080.05960.1574-0.0623-0.11610.0565-0.0029-0.00980.02120.02050.094525.13097.209165.2881
50.73840.18770.22560.07460.03570.1007-0.02980.05280.03370.01040.0150.00050.00090.0120.01470.0542-0.0025-0.00360.05160.00460.032514.439619.158150.5814
61.8482.0101-1.19362.2007-1.18541.70160.0110.07060.01470.02350.09040.00760.04740.0447-0.10140.04740.02780.01760.035-0.00060.04545.196813.861253.9062
74.7589-1.7694-2.47461.8052.52583.5418-0.00180.18990.00760.0194-0.0015-0.00320.0028-0.00310.00330.0827-0.0114-0.01020.0290.00290.013859.45534.503167.8665
80.4454-1.01140.23812.3449-0.73612.3262-0.0534-0.0652-0.05530.13740.18860.14270.0770.144-0.13520.05160.02070.01320.10330.00710.016857.908429.42167.5159
90.35410.15420.34810.07930.16770.36620.0257-0.0797-0.02830.0006-0.0083-0.01240.005-0.0441-0.01740.0637-0.0156-0.00050.07130.01990.030244.007125.486669.0813
100.61450.25010.10730.1555-0.06030.2276-0.01880.03610.01570.00580.02070.0136-0.0128-0.0069-0.00190.05330.00110.00620.03770.00350.036340.152727.652457.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 66
2X-RAY DIFFRACTION2A67 - 108
3X-RAY DIFFRACTION3A109 - 153
4X-RAY DIFFRACTION4A154 - 175
5X-RAY DIFFRACTION5A176 - 307
6X-RAY DIFFRACTION6B43 - 63
7X-RAY DIFFRACTION7B64 - 89
8X-RAY DIFFRACTION8B90 - 114
9X-RAY DIFFRACTION9B115 - 166
10X-RAY DIFFRACTION10B167 - 307

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