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- PDB-3kjj: Crystal structure of NMB1025, a member of YjgF protein family, fr... -

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Basic information

Entry
Database: PDB / ID: 3kjj
TitleCrystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (hexagonal crystal form)
ComponentsNMB1025 protein
KeywordsUNKNOWN FUNCTION / NMB1025 / YjgF protein family / Neisseria meningitidis / OPPF / Structural Genomics / Oxford Protein Production Facility
Function / homology
Function and homology information


RutC family, YoaB-like / RidA, conserved site / Uncharacterized protein family UPF0076 signature. / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRen, J. / Sainsbury, S. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: To be Published
Title: Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis
Authors: Ren, J. / Sainsbury, S. / Owens, R.J.
History
DepositionNov 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NMB1025 protein
B: NMB1025 protein
C: NMB1025 protein
D: NMB1025 protein
E: NMB1025 protein
F: NMB1025 protein
G: NMB1025 protein
H: NMB1025 protein
I: NMB1025 protein
J: NMB1025 protein
K: NMB1025 protein
L: NMB1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,30214
Polymers173,11812
Non-polymers1842
Water14,430801
1
A: NMB1025 protein
B: NMB1025 protein
C: NMB1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4645
Polymers43,2793
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-37 kcal/mol
Surface area13600 Å2
MethodPISA
2
D: NMB1025 protein
E: NMB1025 protein
F: NMB1025 protein


Theoretical massNumber of molelcules
Total (without water)43,2793
Polymers43,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-39 kcal/mol
Surface area13250 Å2
MethodPISA
3
G: NMB1025 protein
H: NMB1025 protein
I: NMB1025 protein


Theoretical massNumber of molelcules
Total (without water)43,2793
Polymers43,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-39 kcal/mol
Surface area13200 Å2
MethodPISA
4
J: NMB1025 protein

J: NMB1025 protein

J: NMB1025 protein


Theoretical massNumber of molelcules
Total (without water)43,2793
Polymers43,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6990 Å2
ΔGint-34 kcal/mol
Surface area13730 Å2
MethodPISA
5
K: NMB1025 protein

K: NMB1025 protein

K: NMB1025 protein


Theoretical massNumber of molelcules
Total (without water)43,2793
Polymers43,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6820 Å2
ΔGint-38 kcal/mol
Surface area13690 Å2
MethodPISA
6
L: NMB1025 protein

L: NMB1025 protein

L: NMB1025 protein


Theoretical massNumber of molelcules
Total (without water)43,2793
Polymers43,2793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6270 Å2
ΔGint-42 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.613, 155.613, 116.189
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11K-696-

HOH

21L-695-

HOH

31L-751-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

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Components

#1: Protein
NMB1025 protein


Mass: 14426.478 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: NMB1025 / Plasmid: OPPF1359 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JZJ4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0
Temp details: di-Potassium Hydrogen Phosphate 1.2 M, Sodium di-Hydrogen Phosphate 0.6 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.422
11h+k,-k,-l20.578
ReflectionResolution: 1.9→30 Å / Num. obs: 126653 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 27.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 31.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 3.2 / Num. unique all: 12608 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.839 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20629 6478 5.1 %RANDOM
Rwork0.16574 ---
obs0.1678 120095 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.636 Å2
Baniso -1Baniso -2Baniso -3
1--14.07 Å20 Å20 Å2
2---14.07 Å20 Å2
3---28.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10893 0 12 801 11706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.93615271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.651425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85722.825538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.644151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.13315124
X-RAY DIFFRACTIONr_chiral_restr0.0710.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218696
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.76947008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.751811170
X-RAY DIFFRACTIONr_scbond_it4.01884219
X-RAY DIFFRACTIONr_scangle_it5.257124086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 819 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.4630
Bloose positional0.4530
Cloose positional0.5230
Dloose positional0.5630
Eloose positional0.4330
Floose positional0.430
Gloose positional0.4730
Hloose positional0.3430
Iloose positional0.530
Jloose positional0.430
Kloose positional0.3130
Lloose positional0.6430
Aloose thermal4.1110
Bloose thermal4.3810
Cloose thermal3.1910
Dloose thermal4.9610
Eloose thermal5.3710
Floose thermal3.0110
Gloose thermal5.1110
Hloose thermal4.3310
Iloose thermal3.2810
Jloose thermal4.7610
Kloose thermal3.2910
Lloose thermal11.110
LS refinement shellResolution: 1.9→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 449 -
Rwork0.399 7793 -
obs--87.55 %

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