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- PDB-9evf: Citramalate lyase - ADP - pyruvate complex -

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Basic information

Entry
Database: PDB / ID: 9evf
TitleCitramalate lyase - ADP - pyruvate complex
Components(Citramalate lyase, subunit ...) x 2
KeywordsLYASE / ATP / citramalate / aldolase / glutamate fermentation
Function / homologyADENOSINE-5'-DIPHOSPHATE / PYRUVIC ACID
Function and homology information
Biological speciesRaoultella planticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsErmler, U. / Berg, I. / Demmer, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Novel citramalate lyase involved in glutamate fermentation of enterobacteria
Authors: Eggers, J. / Schaefer, L. / Cassens, E.A. / Schmid, L. / Simon, S.A. / Probst, A.J. / Koenig, S. / Demmer, U. / Ermler, U. / Berg, I.A.
History
DepositionMar 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citramalate lyase, subunit A (cmlA)
B: Citramalate lyase, subunit B (cmlB)
C: Citramalate lyase, subunit A (cmlA)
D: Citramalate lyase, subunit B (cmlB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,86117
Polymers121,9174
Non-polymers1,94413
Water15,043835
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-124 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.210, 108.340, 98.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-929-

HOH

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Components

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Citramalate lyase, subunit ... , 2 types, 4 molecules ACBD

#1: Protein Citramalate lyase, subunit A (cmlA)


Mass: 48954.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella planticola (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein Citramalate lyase, subunit B (cmlB)


Mass: 12003.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella planticola (bacteria) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 6 types, 848 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEP 629, MES pH 6.5, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 222571 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.1 / Net I/σ(I): 12.66
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.4-1.53.781408270.6544.1211
1.5-1.71.21560960.9631.3081
1.7-20.306478980.9880.3351
2-2.50.101375210.9940.1111
2.5-3.30.057224860.9960.0631
3.3-4.50.046105990.9980.051
4.5-5.70.04235670.9980.0451
5.7-80.0422530.9980.0431
8-120.0359300.9990.0391
12-500.0363940.9990.041

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.1 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 10889 4.91 %
Rwork0.178 --
obs0.1788 221951 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8570 0 119 835 9524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.191
X-RAY DIFFRACTIONf_dihedral_angle_d14.4293362
X-RAY DIFFRACTIONf_chiral_restr0.0881363
X-RAY DIFFRACTIONf_plane_restr0.0081634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.42943550.4326834X-RAY DIFFRACTION97
1.42-1.430.44143420.3916875X-RAY DIFFRACTION97
1.43-1.450.40233070.38136965X-RAY DIFFRACTION97
1.45-1.470.39823830.38016825X-RAY DIFFRACTION97
1.47-1.490.39293770.36826878X-RAY DIFFRACTION98
1.49-1.510.36663420.32536926X-RAY DIFFRACTION98
1.51-1.530.33923420.29146934X-RAY DIFFRACTION98
1.53-1.550.29394070.27136904X-RAY DIFFRACTION98
1.55-1.580.26613990.25116885X-RAY DIFFRACTION98
1.58-1.60.27963640.22686966X-RAY DIFFRACTION98
1.6-1.630.23733810.21556899X-RAY DIFFRACTION98
1.63-1.660.24513450.20967013X-RAY DIFFRACTION99
1.66-1.690.25534060.20096965X-RAY DIFFRACTION99
1.69-1.730.23833270.19557050X-RAY DIFFRACTION99
1.73-1.760.19743690.19257009X-RAY DIFFRACTION99
1.76-1.80.23073830.20077011X-RAY DIFFRACTION99
1.8-1.850.21723690.18657019X-RAY DIFFRACTION99
1.85-1.90.19494020.17686997X-RAY DIFFRACTION99
1.9-1.960.19883490.17037074X-RAY DIFFRACTION99
1.96-2.020.19813210.17147089X-RAY DIFFRACTION99
2.02-2.090.20573430.17887102X-RAY DIFFRACTION99
2.09-2.170.19783440.16937107X-RAY DIFFRACTION99
2.17-2.270.19013310.16157148X-RAY DIFFRACTION100
2.27-2.390.16773450.16197154X-RAY DIFFRACTION100
2.39-2.540.17413080.16027180X-RAY DIFFRACTION100
2.54-2.740.18983300.16577199X-RAY DIFFRACTION99
2.74-3.020.1853680.17327172X-RAY DIFFRACTION100
3.02-3.450.17484000.1697189X-RAY DIFFRACTION100
3.45-4.350.15184190.14467225X-RAY DIFFRACTION100
4.35-38.10.16254310.1517468X-RAY DIFFRACTION99

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