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- PDB-9jn5: Crystal structure of KtzT-C197A in complex with HEME and substrate -

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Basic information

Entry
Database: PDB / ID: 9jn5
TitleCrystal structure of KtzT-C197A in complex with HEME and substrate
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 / N~5~-hydroxy-L-ornithine / FMN-binding protein
Function and homology information
Biological speciesKutzneria sp. 744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
A: FMN-binding protein
B: FMN-binding protein
C: FMN-binding protein
D: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,76010
Polymers92,9974
Non-polymers2,7626
Water13,403744
1
A: FMN-binding protein
D: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8805
Polymers46,4992
Non-polymers1,3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-74 kcal/mol
Surface area17790 Å2
MethodPISA
2
B: FMN-binding protein
C: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8805
Polymers46,4992
Non-polymers1,3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-74 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.688, 101.088, 110.977
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
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: Chemical ChemComp-ONH / N~5~-hydroxy-L-ornithine


Type: L-peptide linking / Mass: 148.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 55.03 %
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: Sep 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 67091 / % possible obs: 97.6 % / Redundancy: 5.4 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.054 / Rrim(I) all: 0.125 / Χ2: 1.152 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.01-2.084.40.57765090.8950.9720.3030.6550.65196.1
2.08-2.175.10.42966210.960.990.2070.4780.73797.3
2.17-2.265.70.35366640.9750.9940.1590.3880.83797.8
2.26-2.385.70.28466060.9830.9960.1270.3120.91997.3
2.38-2.535.60.2366320.9880.9970.1040.2531.05897
2.53-2.735.30.18166390.990.9980.0860.2011.28197.3
2.73-35.50.1367770.9950.9990.0610.1441.36198.6
3-3.435.60.09968330.9960.9990.0460.1091.47599.6
3.43-4.325.50.07468500.9970.9990.0350.0821.5898.3
4.32-255.20.06469600.9960.9990.0320.0711.44996.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.196 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30242 3309 5 %RANDOM
Rwork0.24008 ---
obs0.24315 63521 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.493 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å2-0 Å2
2---2.35 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 192 744 7363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136829
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176281
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6939376
X-RAY DIFFRACTIONr_angle_other_deg1.361.60214378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56919.13368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58615929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5721576
X-RAY DIFFRACTIONr_chiral_restr0.070.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027913
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021643
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_it2.5633.0683403
X-RAY DIFFRACTIONr_mcbond_other2.5623.0683403
X-RAY DIFFRACTIONr_mcangle_it3.764.5834245
X-RAY DIFFRACTIONr_mcangle_other3.764.5844246
X-RAY DIFFRACTIONr_scbond_it2.9093.3163426
X-RAY DIFFRACTIONr_scbond_other2.9093.3163426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5244.8365132
X-RAY DIFFRACTIONr_long_range_B_refined6.936.7938071
X-RAY DIFFRACTIONr_long_range_B_other6.936.7968072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 219 -
Rwork0.34 4204 -
obs--87.34 %

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