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- PDB-7kou: 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Bi... -

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Entry
Database: PDB / ID: 7kou
Title1.83 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 superfamily / DI(HYDROXYETHYL)ETHER / Oxidoreductase
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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: 1.83 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 10, 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

Downloads & links

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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)66,35819
Polymers65,5624
Non-polymers79515
Water12,178676
1
A: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4955
Polymers16,3911
Non-polymers1044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4724
Polymers16,3911
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6545
Polymers16,3911
Non-polymers2634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7375
Polymers16,3911
Non-polymers3464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.928, 62.022, 101.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 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

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Non-polymers , 5 types, 691 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
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: JCSG+ (F8), 2.1M DL-Malic acid pH 7.0; Cryo: 25% PEG 400, 1.5M DL-Malic acid 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: 1.83→30 Å / Num. obs: 68046 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.04 / Rrim(I) all: 0.093 / Rsym value: 0.084 / Χ2: 1.015 / Net I/σ(I): 19.4
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3378 / CC1/2: 0.78 / CC star: 0.936 / Rpim(I) all: 0.367 / Rrim(I) all: 0.857 / Rsym value: 0.773 / Χ2: 1.006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7kom

7kom


Resolution: 1.83→29.8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.613 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 3422 5 %RANDOM
Rwork0.1619 ---
obs0.1635 64577 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.01 Å2 / Biso mean: 23.732 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0 Å20 Å2
2---1.09 Å20 Å2
3---2.35 Å2
Refinement stepCycle: final / Resolution: 1.83→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 45 735 5326
Biso mean--53.93 36.24 -
Num. residues----586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134851
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174576
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6466614
X-RAY DIFFRACTIONr_angle_other_deg0.3581.57710647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4265623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69423.744219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9715823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2611520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.025475
X-RAY DIFFRACTIONr_gen_planes_other0.0530.02953
LS refinement shellResolution: 1.832→1.879 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 239 -
Rwork0.269 4567 -
all-4806 -
obs--96.51 %
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)
111.64592.155-2.12931.019-0.4711.22760.09410.18350.3487-0.0694-0.02720.0531-0.0711-0.1152-0.06680.0318-0.00210.0030.057-0.00940.040617.400919.4843-8.9618
23.75061.1608-0.0723.51710.34271.35190.03830.16080.1103-0.3088-0.04610.1345-0.0939-0.14070.00780.04630.01970.00520.02560.0050.02517.9422.1509-2.1634
32.70370.3037-1.57991.5619-0.59888.13380.0691-0.0676-0.06440.0876-0.08720.14630.23850.26370.01810.02070.00360.02160.0120.0010.119513.542511.37513.8428
46.46984.8072-3.68593.8218-2.26364.22310.2336-0.1239-0.0650.1374-0.13350.03940.0196-0.1209-0.10010.09250.009-0.02180.05790.03620.166613.030410.468714.5068
52.9822-0.518-0.98873.71460.48090.92620.0090.01770.0203-0.0295-0.0510.04470.03910.05210.0420.01840.0022-0.00030.00840.00770.026319.932225.31768.0535
63.3489-1.58551.77099.2972-3.83991.99240.09840.0903-0.0539-0.109-0.169-0.26880.07090.10130.07070.04160.00330.00990.061-0.00830.03426.738118.614815.3236
71.0097-0.05720.2011.8507-0.32921.05030.0489-0.0802-0.02880.18960.01530.13840.0012-0.0922-0.06410.0453-0.00060.03870.0243-0.00720.072413.046518.708914.3115
815.56970.09211.42010.75510.66473.6191-0.0382-0.1471-0.48830.17510.0707-0.0122-0.0856-0.0885-0.03250.06220.019-0.00470.04670.0110.036115.504145.177159.0341
95.8084-1.460.41882.0340.43931.99190.035-0.2901-0.15380.15380.0080.04870.0611-0.1511-0.04290.0306-0.0029-0.00850.03070.00880.01117.406141.12653.0147
101.71050.16392.22552.21080.41766.4162-0.119-0.0550.0775-0.07040.0021-0.0278-0.184-0.09640.1170.01650.01240.01910.0629-0.01660.131211.545751.68438.2456
116.473-4.45414.20213.0684-2.91484.1253-0.05420.07920.2230.044-0.0562-0.166-0.03520.03040.11030.0244-0.0228-0.00210.0233-0.00860.105415.3651.470439.6388
124.4641.51071.28793.66440.98650.48680.03380.0613-0.16970.123-0.01490.11090.05620.0401-0.01890.06050.02040.0080.06530.02190.086118.202436.329942.7682
133.89710.495-1.48167.5026-3.25792.0468-0.01190.03680.0570.0109-0.0323-0.22740.00180.10270.04430.0144-0.002-0.00460.0712-0.00140.033424.78344.606135.547
140.53680.23590.10811.0165-0.48951.24670.03920.03570.0449-0.1076-0.0067-0.00340.0593-0.1039-0.03240.0250.0044-0.00040.0388-0.00810.070411.885244.558636.3607
155.23342.91822.41292.90544.37078.3097-0.09090.05330.1357-0.14470.13960.0113-0.25220.3071-0.04870.01420.00520.01170.05080.00430.062735.318219.963736.7484
162.4999-0.01560.38741.91650.99593.57850.12080.05120.1141-0.1147-0.0433-0.2786-0.03520.1707-0.07750.0177-00.01450.05460.00060.06829.08920.238940.3908
176.6032-0.3128-0.05065.2328-0.38792.30420.14260.0611-0.11320.1663-0.1538-0.16120.0147-0.03060.01130.03150.0009-0.00530.0266-0.02720.058112.44256.214744.3946
184.35584.32712.89034.94623.47962.555-0.0025-0.1017-0.23590.09080.0385-0.15430.08950.1118-0.0360.06760.0173-0.01590.09490.01250.151921.573611.18246.9147
191.7560.14880.14644.2376-1.59133.78860.1144-0.09620.02910.2133-0.1070.09860.07220.091-0.00740.0251-0.00110.00350.0421-0.02990.050416.944721.779749.0523
201.2389-0.0480.6931.7968-1.0774.0128-0.05480.103-0.1865-0.17120.0369-0.08920.04610.11350.01790.0209-0.01270.02440.0324-0.05170.098116.26138.697136.6597
211.59980.2404-0.00342.8235-0.12041.17190.0404-0.0715-0.01430.1599-0.05690.25320.034-0.060.01640.01620.00210.00570.0223-0.02580.084611.837816.241446.428
2210.1612-1.7895-7.0342.13464.912812.4503-0.1128-0.5904-0.52980.22910.1428-0.16930.51240.5473-0.030.06510.0004-0.00260.09610.04960.191635.115745.186313.9169
233.2554-0.1676-1.30692.84891.13952.44410.0612-0.1214-0.01330.0758-0.0342-0.20950.05940.0458-0.0270.01670.00730.00110.01720.01540.035628.053244.614410.343
246.48830.89362.66433.00051.09471.9406-0.17970.25730.4346-0.225-0.09350.0868-0.22210.01390.27320.0840.0095-0.02610.02130.00820.1119.858758.31547.3127
252.29050.8208-1.12952.685-0.47631.13740.04840.0724-0.0152-0.0205-0.04470.047-0.0028-0.0245-0.00370.01490.0041-0.00250.01090.00310.05519.732742.25544.2614
263.9718-2.48831.618610.1921-4.15977.66060.06470.4231-0.0286-0.4591-0.2425-0.2293-0.00580.24870.17780.04980.00850.01550.06310.02660.058916.804247.8499-5.0038
271.3526-0.2241-0.32181.0217-0.59155.0286-0.0442-0.130.21150.11140.0239-0.0141-0.10110.04580.02040.0261-0.0007-0.00290.0144-0.02050.066614.29154.665114.0552
281.5922-0.2222-0.07441.93790.06730.90880.02840.14460.0301-0.1668-0.05350.1883-0.0297-0.05060.02510.02870.0007-0.00450.0185-0.00340.074810.422947.04474.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 31
2X-RAY DIFFRACTION2A32 - 56
3X-RAY DIFFRACTION3A57 - 71
4X-RAY DIFFRACTION4A72 - 83
5X-RAY DIFFRACTION5A84 - 109
6X-RAY DIFFRACTION6A110 - 117
7X-RAY DIFFRACTION7A118 - 168
8X-RAY DIFFRACTION8B23 - 31
9X-RAY DIFFRACTION9B32 - 54
10X-RAY DIFFRACTION10B55 - 72
11X-RAY DIFFRACTION11B73 - 87
12X-RAY DIFFRACTION12B88 - 107
13X-RAY DIFFRACTION13B108 - 117
14X-RAY DIFFRACTION14B118 - 168
15X-RAY DIFFRACTION15C23 - 31
16X-RAY DIFFRACTION16C32 - 59
17X-RAY DIFFRACTION17C60 - 72
18X-RAY DIFFRACTION18C73 - 91
19X-RAY DIFFRACTION19C92 - 117
20X-RAY DIFFRACTION20C118 - 133
21X-RAY DIFFRACTION21C134 - 168
22X-RAY DIFFRACTION22D22 - 31
23X-RAY DIFFRACTION23D32 - 60
24X-RAY DIFFRACTION24D61 - 79
25X-RAY DIFFRACTION25D80 - 109
26X-RAY DIFFRACTION26D110 - 117
27X-RAY DIFFRACTION27D118 - 132
28X-RAY DIFFRACTION28D133 - 168

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