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- PDB-6y01: The structure of the molybdenum cofactor binding protein from the... -

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Basic information

Entry
Database: PDB / ID: 6y01
TitleThe structure of the molybdenum cofactor binding protein from the phototrophic bacterium Rippkaea orientalis
Componentsp450 cytochrome, putative
KeywordsTRANSPORT PROTEIN / molybdenum cofactor / Moco / ligand binding / Rossmann fold
Function / homologyConserved hypothetical protein CHP00725 / SLOG cluster4 / SLOG cluster4 family / IMIDAZOLE / p450 cytochrome, putative
Function and homology information
Biological speciesRippkaea orientalis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsKrausze, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The structure of the Moco carrier protein from Rippkaea orientalis.
Authors: Krausze, J. / Hercher, T.W. / Archna, A. / Kruse, T.
History
DepositionFeb 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: p450 cytochrome, putative
BBB: p450 cytochrome, putative
CCC: p450 cytochrome, putative
DDD: p450 cytochrome, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,06716
Polymers75,5754
Non-polymers49312
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-182 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.577, 72.044, 70.264
Angle α, β, γ (deg.)90.000, 113.333, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
p450 cytochrome, putative


Mass: 18893.697 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rippkaea orientalis (strain PCC 8801) (bacteria)
Gene: PCC8801_2644 / Plasmid: pQE80 / Cell line (production host): RK5204 / Production host: Escherichia coli (E. coli) / References: UniProt: B7K4Z0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.88 % / Description: rod-like, monoclinic
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% (v/v) Pentaerythritol ethoxylate; 0.2 M potassium acetate; 3% (v/v) Jeffamine T-403; 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 17, 2015 / Details: TOROIDAL FOCUSING MIRRORS
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.23→64.52 Å / Num. obs: 181674 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 15.66 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05279 / Rpim(I) all: 0.02177 / Rrim(I) all: 0.05719 / Net I/σ(I): 16.35
Reflection shellResolution: 1.23→1.274 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.026 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 18104 / CC1/2: 0.193 / CC star: 0.569 / Rpim(I) all: 1.297 / Rrim(I) all: 3.299 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSJun 1, 2017data processing
Aimless0.7.4data scaling
PHASER2.5.6phasing
SHELXE2014/4model building
Coot0.8.9.2model building
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZ6

2iz6


Resolution: 1.23→64.518 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 3.314 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions. Paired refinement was carried out to evaluate the proper high-resolution limit.
RfactorNum. reflection% reflectionSelection details
Rfree0.1629 8868 4.88 %RANDOM
Rwork0.1418 ---
all0.143 ---
obs-181736 99.999 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 27.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.509 Å20 Å23.035 Å2
2---3.184 Å20 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 1.23→64.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 20 393 5187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0134906
X-RAY DIFFRACTIONr_bond_other_d0.0070.0174712
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6126690
X-RAY DIFFRACTIONr_angle_other_deg1.6911.56410942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03125.86186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62115834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.841513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025546
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02825
X-RAY DIFFRACTIONr_nbd_refined0.2340.21031
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24615
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.226
X-RAY DIFFRACTIONr_nbd_other0.2820.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.215
X-RAY DIFFRACTIONr_mcbond_it2.2662.7472663
X-RAY DIFFRACTIONr_mcbond_other2.2642.7452662
X-RAY DIFFRACTIONr_mcangle_it2.7044.1293334
X-RAY DIFFRACTIONr_mcangle_other2.7054.1323335
X-RAY DIFFRACTIONr_scbond_it3.3353.2012243
X-RAY DIFFRACTIONr_scbond_other3.3343.2032244
X-RAY DIFFRACTIONr_scangle_it3.9174.6533356
X-RAY DIFFRACTIONr_scangle_other3.9174.6553357
X-RAY DIFFRACTIONr_lrange_it4.12135.6745492
X-RAY DIFFRACTIONr_lrange_other4.02335.3485424
X-RAY DIFFRACTIONr_rigid_bond_restr5.01339618
X-RAY DIFFRACTIONr_ncsr_local_group_10.0810.054928
X-RAY DIFFRACTIONr_ncsr_local_group_20.0880.054867
X-RAY DIFFRACTIONr_ncsr_local_group_30.0990.054819
X-RAY DIFFRACTIONr_ncsr_local_group_40.0790.054927
X-RAY DIFFRACTIONr_ncsr_local_group_50.1070.054846
X-RAY DIFFRACTIONr_ncsr_local_group_60.1080.054824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.23-1.2620.3486360.354127720.353134080.8520.8381000.356
1.262-1.2960.3276210.322124450.322130660.8390.8521000.323
1.296-1.3340.315710.299121050.3126770.8660.86799.99210.297
1.334-1.3750.2846660.284116560.284123220.8830.8991000.277
1.375-1.420.2695910.253113640.253119550.8980.9171000.241
1.42-1.470.245770.214110110.216115880.9230.9421000.193
1.47-1.5250.1914960.176107120.176112080.9520.9621000.15
1.525-1.5880.1715260.147101870.148107130.9660.9731000.121
1.588-1.6580.1624930.13898280.14103220.970.97699.99030.114
1.658-1.7390.1634970.12693520.12898490.9740.981000.104
1.739-1.8330.1375240.11288690.11493930.9780.9831000.093
1.833-1.9440.1444220.10384710.10588930.9730.9861000.088
1.944-2.0780.1414200.11179180.11283380.9770.9831000.1
2.078-2.2440.1423700.1174330.11178030.9790.9831000.103
2.244-2.4580.1244050.167620.10171670.9820.9871000.096
2.458-2.7480.1383410.10961520.11164930.9790.9851000.109
2.748-3.1720.1592760.1354670.13257430.970.9761000.136
3.172-3.8830.1471770.12646940.12748710.9770.981000.139
3.883-5.4810.1261680.12136210.12237890.9830.9831000.14
5.481-64.5180.173910.17120480.17121390.9660.9681000.195

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