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- PDB-4m54: The structure of the staphyloferrin B precursor biosynthetic enzy... -

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Basic information

Entry
Database: PDB / ID: 4m54
TitleThe structure of the staphyloferrin B precursor biosynthetic enzyme SbnB bound to N-(1-amino-1-carboxyl-2-ethyl)-glutamic acid and NADH
ComponentsPutative ornithine cyclodeaminase
KeywordsLyase/lyase Inhibitor / siderophore / iron / L-2 / 3-diaminopropionic acid synthesis / NAD(P) binding Rossmann fold / Lyase-lyase Inhibitor complex
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / siderophore biosynthetic process / nucleotide binding
Similarity search - Function
2,3-diaminopropionate biosynthesis protein SbnB / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / Ig-like domain profile. / Immunoglobulin-like domain / NAD(P)-binding domain superfamily ...2,3-diaminopropionate biosynthesis protein SbnB / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / Ig-like domain profile. / Immunoglobulin-like domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 2,3-diaminopropionate biosynthesis protein SbnB / Putative ornithine cyclodeaminase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsKobylarz, M.J. / Murphy, M.E.P.
CitationJournal: Chem.Biol. / Year: 2014
Title: Synthesis of L-2,3-diaminopropionic acid, a siderophore and antibiotic precursor.
Authors: Kobylarz, M.J. / Grigg, J.C. / Takayama, S.J. / Rai, D.K. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Putative ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0084
Polymers38,0731
Non-polymers9353
Water1,69394
1
A: Putative ornithine cyclodeaminase
hetero molecules

A: Putative ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0168
Polymers76,1462
Non-polymers1,8706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area7020 Å2
ΔGint-65 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.116, 63.116, 159.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative ornithine cyclodeaminase /


Mass: 38072.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NEWMAN / Gene: sbnB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NYS7, UniProt: A0A0H3K9Y6*PLUS
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AE5 / N-[(2S)-2-amino-2-carboxyethyl]-L-glutamic acid


Type: L-peptide linking / Mass: 234.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N2O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 0.2 M MgCl2, 29-33% PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 18, 2013 / Details: VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→29.73 Å / Num. obs: 13956 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 32.59 Å2 / Rmerge(I) obs: 0.126 / Χ2: 0.954 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.36-2.45.30.596680.679198.7
2.4-2.446.60.5416800.7391100
2.44-2.4970.5536750.7811100
2.49-2.547.10.486890.785199.9
2.54-2.67.20.4776800.8231100
2.6-2.6670.4136870.806199.9
2.66-2.726.90.3656800.864199.4
2.72-2.86.80.3216690.89199.4
2.8-2.886.60.2627080.901199.6
2.88-2.976.70.2346690.951198.8
2.97-3.086.50.2036861.01199.1
3.08-3.26.50.196781.047198.4
3.2-3.356.40.1456991.057199.4
3.35-3.536.30.146971.224199.9
3.53-3.756.30.1067061.2451100
3.75-4.036.50.1047021.1361100
4.03-4.447.20.0817151.118199.6
4.44-5.087.90.0687250.9931100
5.08-6.48.30.087500.9591100
6.4-508.10.0557931.018196.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2-1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.8.2-1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→29.726 Å / Occupancy max: 1 / Occupancy min: 0.87 / FOM work R set: 0.8013 / SU ML: 0.3 / σ(F): 1.33 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1383 10 %RANDOM
Rwork0.2234 ---
obs0.2269 13833 99.02 %-
all-13910 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.14 Å2 / Biso mean: 37.5823 Å2 / Biso min: 11.26 Å2
Refinement stepCycle: LAST / Resolution: 2.36→29.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 61 94 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022555
X-RAY DIFFRACTIONf_angle_d0.7033467
X-RAY DIFFRACTIONf_chiral_restr0.048387
X-RAY DIFFRACTIONf_plane_restr0.002450
X-RAY DIFFRACTIONf_dihedral_angle_d14.163945
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3594-2.44370.30461340.25911209134399
2.4437-2.54150.31291350.261312251360100
2.5415-2.65710.3151370.257512271364100
2.6571-2.79710.36571350.24971206134199
2.7971-2.97220.28411370.24571236137399
2.9722-3.20150.25171350.23821231136699
3.2015-3.52320.26411370.23421221135898
3.5232-4.03190.2511370.21591237137498
4.0319-5.07570.19031430.17211280142399
5.0757-29.72860.24431530.222113781531100
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)
15.0657-0.3666-1.49432.27660.36251.2730.01450.489-0.20150.0386-0.0971-0.2682-0.08950.11090.09280.2549-0.0557-0.04330.31210.06460.1821-20.971328.3087-11.0284
24.13911.01830.07553.8747-1.14033.9505-0.0829-0.0038-0.13140.1314-0.084-0.48470.09250.20560.10430.15380.0508-0.01420.17270.00230.2354-21.499932.5201-0.0311
33.9427-0.33070.67383.2031-2.09441.2864-0.16160.3586-0.4477-0.05990.0769-0.0684-0.18350.07230.08810.2164-0.03680.05140.202-0.03980.3049-5.015917.8467-6.4553
43.6320.46870.19993.8232-1.30993.0265-0.0303-0.1137-0.49380.3630.0566-0.29280.02590.1374-0.02180.24270.0021-0.02810.27680.04680.3342.291820.4062-0.5195
58.1577-0.97221.82485.0578-1.97074.2275-0.17830.67590.48160.10080.02690.1711-0.46820.1402-0.01540.2203-0.0428-0.02080.22690.04340.2257-0.625333.1367-13.6347
63.53330.3909-1.57012.40350.62721.92850.09280.2969-0.505-0.3493-0.3230.08040.1078-0.23650.19150.30920.0252-0.07070.29190.0280.2626-29.682226.6788-10.7743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 46 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 115 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 174 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 253 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 309 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 336 )A0

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