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- PDB-4mp8: Staphyloferrin B precursor biosynthetic enzyme SbnB bound to malo... -

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Basic information

Entry
Database: PDB / ID: 4mp8
TitleStaphyloferrin B precursor biosynthetic enzyme SbnB bound to malonate and NAD+
ComponentsPutative ornithine cyclodeaminase
KeywordsOXIDOREDUCTASE / siderophore / L-Dap synthesis / ACEGA dehydrogenase
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
MALONATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,3-diaminopropionate biosynthesis protein SbnB / Putative ornithine cyclodeaminase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGrigg, J.C. / Kobylarz, M.J. / Rai, D.K. / 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
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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)38,8383
Polymers38,0731
Non-polymers7652
Water2,540141
1
A: Putative ornithine cyclodeaminase
hetero molecules

A: Putative ornithine cyclodeaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6776
Polymers76,1462
Non-polymers1,5314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7370 Å2
ΔGint-31 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.402, 62.402, 157.687
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2011
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→58 Å / Num. obs: 27690 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3
Reflection shellHighest resolution: 1.84 Å / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→58 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2169 / WRfactor Rwork: 0.1758 / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8715 / SU B: 6.381 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1539 / SU Rfree: 0.1399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1385 5 %RANDOM
Rwork0.1842 ---
obs0.1862 26080 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.88 Å2 / Biso mean: 30.4059 Å2 / Biso min: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.85→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 51 141 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192789
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9643790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95925.29138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67415481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9261514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212138
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.268 -
Rwork0.233 1690
all-1777
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)
11.4776-0.16150.230.49410.0890.2927-0.00130.14060.1664-0.0047-0.02960.00540.03550.01540.03090.1423-0.00410.00570.13440.00240.1145-10.0874.4694-11.2374
20.54760.241-0.3430.8050.48020.85730.0024-0.03020.0626-0.0525-0.01340.15090.0026-0.01010.0110.14330.03450.00240.1575-0.01050.1454-12.1355-1.04872.6896
32.0174-0.8855-0.08790.4434-0.0250.1493-0.14620.0330.27170.05820.0652-0.15270.0309-0.04060.0810.15380.0144-0.03710.1536-0.00420.1592-22.410412.3667-5.9257
42.1408-0.8126-0.00770.72940.01730.0073-0.1761-0.09270.00090.11220.14250.0579-0.004-0.00390.03350.15170.0254-0.01110.13480.00040.1457-32.708410.3958-1.9653
56.7988-4.0001-1.55229.58894.30344.9766-1.4513-0.9958-2.61820.62580.68950.772-0.46140.56320.76180.47030.14410.46190.17430.42171.1818-32.25-11.2937-2.7172
61.5541-0.38830.05040.20790.06340.1011-0.00460.2049-0.1757-0.0393-0.04060.0196-0.0232-0.00590.04520.14590.0046-0.00640.1657-0.03440.1285-17.34672.459-13.1541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 45
2X-RAY DIFFRACTION2A46 - 105
3X-RAY DIFFRACTION3A106 - 179
4X-RAY DIFFRACTION4A180 - 257
5X-RAY DIFFRACTION5A258 - 277
6X-RAY DIFFRACTION6A278 - 336

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