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- PDB-9jn4: Crystal structure of KtzT-C197A in complex with HEME -

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Basic information

Entry
Database: PDB / ID: 9jn4
TitleCrystal structure of KtzT-C197A in complex with HEME
ComponentsFMN-binding protein
KeywordsOXIDOREDUCTASE / Heme-dependent piperazate synthase
Function / homologyTranscriptional regulator PAI 2-type / Putative FMN-binding domain / FMN-binding split barrel / PROTOPORPHYRIN IX CONTAINING FE / FMN-binding protein
Function and homology information
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLi, Y.L. / Yang, Y.Y. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911400 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Structural Insights into the N-N Bond-Formation Mechanism of the Heme-Dependent Piperazate Synthase KtzT
Authors: Yang, Y. / Li, Y. / Yao, L. / Dai, K. / Fu, X. / Ge, A. / Huang, J.W. / Guo, R.T. / Chen, C.C.
History
DepositionSep 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: FMN-binding protein
D: FMN-binding protein
A: FMN-binding protein
C: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4638
Polymers92,9974
Non-polymers2,4664
Water18,1231006
1
B: FMN-binding protein
D: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7324
Polymers46,4992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-73 kcal/mol
Surface area17810 Å2
MethodPISA
2
A: FMN-binding protein
C: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7324
Polymers46,4992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-76 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.817, 101.256, 111.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
FMN-binding protein / KtzT / Regulator


Mass: 23249.340 Da / Num. of mol.: 4 / Mutation: C197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kutzneria sp. 744 (bacteria) / Gene: KUTG_08928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8CF72
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.1 M ammonium acetate, 0.1 M Tris pH 8.0, 1.0 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→25 Å / Num. obs: 91871 / % possible obs: 98.5 % / Redundancy: 4.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.039 / Rrim(I) all: 0.083 / Χ2: 0.917 / Net I/σ(I): 9.5 / Num. measured all: 383395
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.81-1.873.40.41988100.930.9820.2580.4950.49495.7
1.87-1.953.90.31290630.9660.9910.1740.3580.54998.3
1.95-2.044.20.23591280.980.9950.1270.2680.60398.9
2.04-2.154.30.16691760.990.9980.0890.1890.69199
2.15-2.284.30.13491710.9940.9980.0720.1520.77899.1
2.28-2.4640.10791980.9940.9990.060.1240.95898.8
2.46-2.74.30.08591600.9970.9990.0460.0971.20298.5
2.7-3.094.50.06492480.9980.9990.0330.0721.18398.8
3.09-3.94.50.0593750.99810.0260.0561.29199.4
3.9-254.20.0595420.9970.9990.0270.0571.17697.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→24.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.357 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25272 4588 5 %RANDOM
Rwork0.21346 ---
obs0.21548 87035 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.423 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å2-0 Å2
2---2.05 Å20 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.81→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 172 1006 7610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176258
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.699350
X-RAY DIFFRACTIONr_angle_other_deg1.4271.59514322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72119.13368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51415928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9031576
X-RAY DIFFRACTIONr_chiral_restr0.0820.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027898
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021642
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_it2.1412.1733396
X-RAY DIFFRACTIONr_mcbond_other2.1412.1723395
X-RAY DIFFRACTIONr_mcangle_it3.1283.2494238
X-RAY DIFFRACTIONr_mcangle_other3.1283.254239
X-RAY DIFFRACTIONr_scbond_it2.7112.4033412
X-RAY DIFFRACTIONr_scbond_other2.7112.4033410
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1583.485112
X-RAY DIFFRACTIONr_long_range_B_refined6.25326.8438145
X-RAY DIFFRACTIONr_long_range_B_other6.02425.9837817
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.856 Å
RfactorNum. reflection% reflection
Rfree0.301 282 -
Rwork0.288 5564 -
obs--85.13 %

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