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- PDB-7kos: 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Bi... -

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Entry
Database: PDB / ID: 7kos
Title1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58
ComponentsPterin Binding Protein
KeywordsPterin binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PruR
Function / homologyOxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / FORMIC ACID / alpha-D-glucopyranose / MALONIC ACID / Oxidoreductase molybdopterin-binding domain-containing protein
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Pshenychnyi, S. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein PruR (Atu3496) from Agrobacterium fabrum str. C58.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Pshenychnyi, S. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pterin Binding Protein
B: Pterin Binding Protein
C: Pterin Binding Protein
D: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,70818
Polymers65,5624
Non-polymers1,14614
Water12,106672
1
A: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8256
Polymers16,3911
Non-polymers4345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6685
Polymers16,3911
Non-polymers2774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5183
Polymers16,3911
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6984
Polymers16,3911
Non-polymers3073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.462, 91.810, 99.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
Pterin Binding Protein


Mass: 16390.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu3496 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21.Gold / References: UniProt: A9CFB2
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 684 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 12.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3. Screen: Classics II (C3), 2.4M Sodium malonate pH 7.0 Cryo: 25% Sucrose, 1.2M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 118548 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.051 / Rsym value: 0.046 / Χ2: 1.01 / Net I/σ(I): 31.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5876 / CC1/2: 0.82 / CC star: 0.949 / Rpim(I) all: 0.361 / Rrim(I) all: 0.875 / Rsym value: 0.796 / Χ2: 1.008 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7kom

7kom


Resolution: 1.5→29.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.303 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 5910 5 %RANDOM
Rwork0.1515 ---
obs0.1525 111854 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.09 Å2 / Biso mean: 25.236 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0 Å2
2---0.93 Å20 Å2
3---1.68 Å2
Refinement stepCycle: final / Resolution: 1.5→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 88 736 5405
Biso mean--35.71 37.6 -
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174978
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6527309
X-RAY DIFFRACTIONr_angle_other_deg0.4021.5911552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5735701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87724.177249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.24915897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.861521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.026320
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021170
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 407 -
Rwork0.269 8187 -
all-8594 -
obs--100 %
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)
11.2-0.0107-0.01921.5777-0.68581.64160.04570.2102-0.2659-0.2012-0.02880.05050.2849-0.0649-0.0170.0944-0.0004-0.0150.0548-0.05940.07740.195748.8648-1.5441
21.49870.4395-0.04610.6490.25391.0820.0550.1298-0.08820.0114-0.00740.02360.0612-0.0054-0.04760.01390.0096-0.00050.0186-0.00550.03942.825356.64036.3556
32.8825-1.1604-2.20721.99080.96654.49240.10850.2588-0.1013-0.3091-0.03980.04270.0814-0.014-0.06870.06910.0101-0.02310.0841-0.04360.037139.026255.8064-6.6669
41.3889-0.25630.00821.41530.00191.06990.05210.21950.0028-0.1288-0.04710.04360.0204-0.0452-0.00490.01530.0061-0.0080.0545-0.00460.011840.720562.2179-2.3531
51.77150.18390.59871.9973-1.45643.4120.04920.071-0.3054-0.1553-0.0708-0.19470.3950.29070.02160.05910.04850.02180.04750.00970.09264.573750.216311.6278
62.5849-1.2902-0.87953.05550.93791.96350.0314-0.4570.09110.36360.0412-0.4027-0.10680.326-0.07250.1426-0.0557-0.06510.15920.02120.058361.484559.644931.0405
71.66190.4828-0.26940.8245-0.45581.00180.0555-0.0484-0.03410.0436-0.0628-0.0988-0.0120.14610.00720.0118-0.00040.00210.02160.00150.021958.310559.790815.0619
81.46560.2694-0.55423.3149-1.25751.5470.0954-0.23850.02220.2768-0.0884-0.2404-0.1140.197-0.0070.0475-0.0238-0.0240.0555-0.00690.027659.470960.195825.3532
91.5960.1274-0.29681.7148-0.19290.86990.0486-0.19550.11420.2352-0.0421-0.0902-0.06440.0642-0.00640.0385-0.0158-0.01170.0395-0.01070.014554.058263.558324.172
101.1091-0.2707-0.3791.94511.87462.5742-0.01030.08420.2074-0.1044-0.10360.0562-0.1505-0.13010.11390.06340.0249-0.00270.0567-0.01960.094927.30883.386816.1358
111.4006-1.62410.87973.4339-1.39391.3976-0.0656-0.2257-0.10320.25950.13380.37410.0588-0.1549-0.06820.1423-0.00820.0640.1063-0.00820.082329.376268.659731.9056
122.5762-0.09950.09740.49250.08841.85240.0301-0.07180.15620.0155-0.02730.0285-0.0285-0.156-0.00280.04090.00230.02190.0161-0.00710.045232.913273.13616.9475
131.0611-0.2479-0.13992.23551.18812.7249-0.0212-0.11110.0440.2023-0.06080.12890.0486-0.14910.08210.07690.01140.04140.0251-0.00290.045531.880269.36426.1822
141.1668-0.334-0.17591.30530.36390.9312-0.0672-0.0954-0.0510.22010.00340.10530.0762-0.00080.06380.0524-0.00010.03550.01540.00230.030237.165466.529324.3857
151.87460.7353-0.28131.9283-0.2311.33470.1770.10760.70010.086-0.04080.26-0.36170.114-0.13620.1153-0.01580.08090.02920.03350.295751.892287.62954.8859
163.434-0.13580.05430.7107-0.51121.42080.09870.04690.3906-0.0314-0.0326-0.0382-0.05360.0928-0.06610.0128-0.00030.02520.00830.00210.077951.660577.71695.0951
174.66232.1119-0.52484.0237-0.65576.33720.06270.41370.5184-0.2940.00640.4206-0.1138-0.3418-0.06910.12570.0442-0.00720.13770.14860.247845.170186.7313-8.535
182.24910.0026-0.57231.18750.16160.94850.08010.21520.2674-0.0437-0.00630.0345-0.02470.0386-0.07380.01470.00790.02360.03460.0280.062851.808774.89590.4734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 87
2X-RAY DIFFRACTION2A88 - 110
3X-RAY DIFFRACTION3A111 - 132
4X-RAY DIFFRACTION4A133 - 168
5X-RAY DIFFRACTION5B21 - 54
6X-RAY DIFFRACTION6B55 - 80
7X-RAY DIFFRACTION7B81 - 107
8X-RAY DIFFRACTION8B108 - 132
9X-RAY DIFFRACTION9B133 - 168
10X-RAY DIFFRACTION10C21 - 53
11X-RAY DIFFRACTION11C54 - 80
12X-RAY DIFFRACTION12C81 - 106
13X-RAY DIFFRACTION13C107 - 132
14X-RAY DIFFRACTION14C133 - 168
15X-RAY DIFFRACTION15D23 - 94
16X-RAY DIFFRACTION16D95 - 122
17X-RAY DIFFRACTION17D123 - 136
18X-RAY DIFFRACTION18D137 - 168

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