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- PDB-2ikb: Crystal Structure of a Protein of Unknown Function NMB1012 from N... -

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Basic information

Entry
Database: PDB / ID: 2ikb
TitleCrystal Structure of a Protein of Unknown Function NMB1012 from Neisseria meningitidis
ComponentsHypothetical protein NMB1012
KeywordsStructural genomics / unknown function / Neisseria meningitidis / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


TtsA-like, Glycoside hydrolase family 108 domain / Peptidoglycan binding domain / Glycosyl hydrolase 108 / Predicted Peptidoglycan domain / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Lysozyme-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Li, H. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.7 A crystal structure of a hypothetical protein NMB1012 from Neisseria meningitidis
Authors: Zhang, R. / Li, H. / Bargassa, M. / Joachimiak, A.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein NMB1012
B: Hypothetical protein NMB1012
C: Hypothetical protein NMB1012
D: Hypothetical protein NMB1012


Theoretical massNumber of molelcules
Total (without water)75,7024
Polymers75,7024
Non-polymers00
Water10,034557
1
A: Hypothetical protein NMB1012
C: Hypothetical protein NMB1012


Theoretical massNumber of molelcules
Total (without water)37,8512
Polymers37,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Hypothetical protein NMB1012
D: Hypothetical protein NMB1012


Theoretical massNumber of molelcules
Total (without water)37,8512
Polymers37,8512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-12 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.335, 52.087, 128.874
Angle α, β, γ (deg.)90.00, 90.68, 90.00
Int Tables number4
Space group name H-MP1211
Detailsunknown, probably monomer

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Components

#1: Protein
Hypothetical protein NMB1012


Mass: 18925.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7DDI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% w/v PEG MME2000, 0.1M Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 65867 / Num. obs: 64965 / % possible obs: 98.63 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.744 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.47 / Num. unique all: 5132 / % possible all: 93.61

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→38.38 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.788 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3482 5.1 %RANDOM
Rwork0.19455 ---
all0.19717 64965 --
obs0.19717 64965 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.192 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-1.11 Å2
2---1.89 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.126 Å0.123 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.084 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 0 557 5624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225182
X-RAY DIFFRACTIONr_bond_other_d0.0020.023579
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9156988
X-RAY DIFFRACTIONr_angle_other_deg0.97338564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57122.971276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96115828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1351552
X-RAY DIFFRACTIONr_chiral_restr0.0830.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021202
X-RAY DIFFRACTIONr_nbd_refined0.2360.21212
X-RAY DIFFRACTIONr_nbd_other0.2030.23661
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22552
X-RAY DIFFRACTIONr_nbtor_other0.0850.22649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2399
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.244
X-RAY DIFFRACTIONr_mcbond_it1.2851.53882
X-RAY DIFFRACTIONr_mcbond_other0.2661.51318
X-RAY DIFFRACTIONr_mcangle_it1.525010
X-RAY DIFFRACTIONr_scbond_it2.46732316
X-RAY DIFFRACTIONr_scangle_it3.4164.51978
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 251 -
Rwork0.222 4553 -
obs-4553 93.61 %
Refinement TLS params.Method: refined / Origin x: 48.652 Å / Origin y: 5.296 Å / Origin z: 96.292 Å
111213212223313233
T-0.0242 Å2-0.0028 Å2-0.0049 Å2--0.0203 Å2-0.0034 Å2--0.0085 Å2
L0.0017 °2-0.0136 °2-0.0188 °2-0.3136 °20.008 °2--0.3003 °2
S-0.0191 Å °0.0421 Å °-0.0193 Å °0.1003 Å °0.0117 Å °-0.036 Å °-0.0084 Å °0.0087 Å °0.0074 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 163
4X-RAY DIFFRACTION1B3 - 50
5X-RAY DIFFRACTION1B51 - 101
6X-RAY DIFFRACTION1B102 - 163
7X-RAY DIFFRACTION1C1 - 50
8X-RAY DIFFRACTION1C51 - 100
9X-RAY DIFFRACTION1C101 - 164
10X-RAY DIFFRACTION1D2 - 50
11X-RAY DIFFRACTION1D51 - 100
12X-RAY DIFFRACTION1D101 - 165

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