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- PDB-4jmc: Enduracididine biosynthesis enzyme MppR complexed with pyruvate -

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Basic information

Entry
Database: PDB / ID: 4jmc
TitleEnduracididine biosynthesis enzyme MppR complexed with pyruvate
ComponentsPutative uncharacterized protein mppR
KeywordsUNKNOWN FUNCTION / Acetoacetate decarboxylase-like
Function / homology
Function and homology information


Enduracididine biosynthesis enzyme MppR / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PYRUVIC ACID / Enduracididine biosynthesis enzyme MppR
Similarity search - Component
Biological speciesStreptomyces hygroscopicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsSilvaggi, N.R.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Functional Characterization of MppR, an Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus: Functional Diversity in the Acetoacetate Decarboxylase-like Superfamily.
Authors: Burroughs, A.M. / Hoppe, R.W. / Goebel, N.C. / Sayyed, B.H. / Voegtline, T.J. / Schwabacher, A.W. / Zabriskie, T.M. / Silvaggi, N.R.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein mppR
B: Putative uncharacterized protein mppR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7765
Polymers64,5122
Non-polymers2643
Water8,935496
1
A: Putative uncharacterized protein mppR
B: Putative uncharacterized protein mppR
hetero molecules

A: Putative uncharacterized protein mppR
B: Putative uncharacterized protein mppR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,55310
Polymers129,0244
Non-polymers5286
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area18070 Å2
ΔGint-83 kcal/mol
Surface area36940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.320, 110.320, 87.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative uncharacterized protein mppR


Mass: 32256.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppR / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q643B8
#2: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% PEG 3350, 0.2M (NH4)2SO4, 1-10mM HEPES. Drops contained 2 ul of protein solution at 12-18 mg/mL (~380-750 uM) and 1 ul of crystallization solution, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.72→34.3 Å / Num. all: 65173 / Num. obs: 65173 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.72-1.819.30.4684.193821100
5.44-34.38.50.04333.22177198.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-SAD model refined to 2.2 Angstrom-resolution

Resolution: 1.72→32.332 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 3298 5.06 %RANDOM
Rwork0.157 ---
obs0.1581 65133 99.19 %-
all-65664 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 1.72→32.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 16 496 4400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094135
X-RAY DIFFRACTIONf_angle_d1.2645668
X-RAY DIFFRACTIONf_dihedral_angle_d12.6341470
X-RAY DIFFRACTIONf_chiral_restr0.082590
X-RAY DIFFRACTIONf_plane_restr0.007767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.78190.2523070.19785687X-RAY DIFFRACTION92
1.7819-1.85320.20893530.18146130X-RAY DIFFRACTION100
1.8532-1.93760.21963260.17766194X-RAY DIFFRACTION100
1.9376-2.03970.2113140.16346223X-RAY DIFFRACTION100
2.0397-2.16750.19183390.15266187X-RAY DIFFRACTION100
2.1675-2.33480.23420.1596175X-RAY DIFFRACTION100
2.3348-2.56960.18373140.15686242X-RAY DIFFRACTION100
2.5696-2.94120.2053210.16986264X-RAY DIFFRACTION100
2.9412-3.70480.17593290.16216312X-RAY DIFFRACTION100
3.7048-32.33730.14523530.146421X-RAY DIFFRACTION100
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)
11.59010.0724-0.05780.6278-0.4081.9998-0.07310.22540.2635-0.11710.0291-0.1174-0.54610.2160.00540.2879-0.0438-0.00480.09490.04770.196829.299657.9236-12.172
20.75560.3886-0.22011.66250.03070.74660.00170.16490.3486-0.24220.0193-0.0878-0.3549-0.01070.03670.31350.0045-0.00250.12960.06280.233824.205759.9269-12.479
31.54410.42590.39930.4359-0.23531.34190.09060.14460.0962-0.04430.0216-0.1007-0.09650.139-0.05220.2074-0.00390.01650.1382-0.00030.180725.674752.1289-8.8082
40.92380.1053-0.47091.385-0.41151.0391-0.02490.29170.0579-0.2135-0.01620.1896-0.12240.0143-0.04470.17740.0274-0.04260.22350.02760.187712.085843.7432-17.9133
50.932-0.14960.21811.4116-0.19021.1426-0.07360.08540.3691-0.1452-0.01150.0797-0.49520.0032-0.03950.3696-0.01250.00080.15550.08040.235120.640359.9245-14.2205
61.60140.11530.09451.2966-0.1511.5914-0.0330.1090.3043-0.10460.05050.0039-0.54980.0269-0.01420.3778-0.0098-0.00270.16920.08320.22721.078761.2575-16.1135
71.4431-0.0518-0.9111.0817-0.04272.7651-0.0243-0.0342-0.0126-0.0911-0.04350.18820.0259-0.37210.05130.1284-0.05730.01020.1972-0.01290.17790.310827.4113-3.0905
80.97230.1007-0.22771.4880.11060.82770.0170.2248-0.1746-0.1769-0.0242-0.13840.16830.0154-0.0250.17280.00890.02040.1243-0.05250.112822.156721.5613-15.6024
90.5856-0.02170.15932.331-0.27910.6555-0.03620.127-0.1735-0.16180.05850.0070.1351-0.00090.00780.1688-0.00310.03720.1338-0.04620.151421.501120.773-13.1097
101.08190.4623-0.17970.4595-0.06151.12910.08640.06710.02690.0072-0.05680.0362-0.098-0.0447-0.02240.16570.01560.02690.1132-0.0070.136920.265828.7703-9.0075
110.6406-0.42620.5811.47840.27141.7408-0.01110.17460.0498-0.42170.0179-0.28920.07480.0862-0.13750.1929-0.03130.07350.1933-0.01370.156533.23537.8521-19.3441
120.8850.1097-0.36161.5405-0.18171.3047-0.04050.1307-0.137-0.14870.0415-0.11190.17020.01870.02980.20930.02440.04210.1507-0.04170.178624.839920.7975-13.6644
131.3149-0.0725-0.21151.6928-0.4211.3038-0.03330.1165-0.1274-0.2288-0.0107-0.10360.16310.02440.02340.1960.01980.0480.1293-0.08060.134424.156319.7437-16.7644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 33:110)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 111:142)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 143:168)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 169:190)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 191:233)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 234:295)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 34:55)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 56:110)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 111:142)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 143:168)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 169:190)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 191:233)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 234:295)

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