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- PDB-3lnl: Crystal structure of Staphylococcus aureus protein SA1388 -

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Basic information

Entry
Database: PDB / ID: 3lnl
TitleCrystal structure of Staphylococcus aureus protein SA1388
ComponentsUPF0135 protein SA1388
KeywordsUNKNOWN FUNCTION / PROTEIN SA1388 / SELENOMETHIONINE SAD
Function / homology
Function and homology information


Rubrerythrin, domain 2 - #300 / DUF34/NIF3, bacteria / DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Rubrerythrin, domain 2 / Single Sheet / Alpha-Beta Plaits ...Rubrerythrin, domain 2 - #300 / DUF34/NIF3, bacteria / DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / Alpha-Beta Plaits - #120 / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Rubrerythrin, domain 2 / Single Sheet / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSingh, K.S. / Chruszcz, M. / Zhang, X. / Minor, W. / Zhang, H.
CitationJournal: Bmc Struct.Biol. / Year: 2006
Title: Structure of a Conserved Hypothetical Protein Sa1388 from S. aureus Reveals a Capped Hexameric Toroid with Two Pii Domain Lids and a Dinuclear Metal Center.
Authors: Singh Saikatendu, K. / Zhang, X. / Kinch, L. / Leybourne, M. / Grishin, N.V. / Zhang, H.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 13, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0398
Polymers83,2122
Non-polymers8266
Water12,466692
1
A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules

A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules

A: UPF0135 protein SA1388
B: UPF0135 protein SA1388
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,11624
Polymers249,6376
Non-polymers2,47918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area25780 Å2
ΔGint-515 kcal/mol
Surface area80700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.547, 132.547, 125.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-849-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116B1 - 370
2116A1 - 370

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Components

#1: Protein UPF0135 protein SA1388


Mass: 41606.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: SA1388 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67273
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Description: THE STRUCTURE FACTOR FILE THAT AUTHORS DEPOSITED IS THE NATIVE DATA SET USED IN THE REFINEMENT
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.1 M BIS-TRIS PROPANE, PH 8.5, 0.2 M MGCL2, 30% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2004 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→33.14 Å / Num. obs: 50416 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.043 / Rsym value: 0.05 / Net I/σ(I): 18.01
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 1.96 / Rsym value: 0.249 / % possible all: 73.8

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SOLVEphasing
HKL-3000phasing
REFMAC5.5.0072refinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→33.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.146 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19053 2661 5 %RANDOM
Rwork0.14909 ---
obs0.15117 50201 94.98 %-
all-50201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 42 692 5871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225314
X-RAY DIFFRACTIONr_bond_other_d0.0080.023452
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.967202
X-RAY DIFFRACTIONr_angle_other_deg1.33638538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78726.296243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94315940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.676157
X-RAY DIFFRACTIONr_chiral_restr0.2360.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025887
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02966
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_it0.8271.53280
X-RAY DIFFRACTIONr_mcbond_other0.2521.51346
X-RAY DIFFRACTIONr_mcangle_it1.4825315
X-RAY DIFFRACTIONr_scbond_it2.58732034
X-RAY DIFFRACTIONr_scangle_it4.0614.51887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 1 / Number: 3878 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.315
loose thermal1.4810
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 147 -
Rwork0.211 2972 -
obs--75.14 %
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)
10.6866-0.4412-0.19572.21980.93810.80780.10480.1170.1758-0.2358-0.0599-0.1448-0.1117-0.0514-0.04490.05130.02260.05940.0290.04530.1039-37.505127.487-11.867
22.1988-4.8086-0.880311.0021.79054.35790.4250.12650.5147-1.0306-0.0557-0.6368-0.6635-0.4608-0.36930.3854-0.0227-0.04230.49090.30.6247-62.811125.13-36.19
30.7067-0.0351-0.27831.51890.08310.69650.070.14610.0058-0.1669-0.0267-0.1182-0.0061-0.0333-0.04330.04190.00960.03730.05290.0010.063-33.74107.928-12.751
41.24530.47390.09711.29380.24340.74890.0401-0.0862-0.14550.1188-0.0750.030.0288-0.03540.0350.0155-0.00280.0160.0180.01680.0594-48.64688.1512.861
55.44041.14131.14012.46120.55296.14570.2535-0.5811-0.64150.32-0.11570.13440.5553-0.8525-0.13770.2288-0.03880.11040.16810.11610.2693-70.467103.14742.87
60.9350.4859-0.21021.4013-0.40080.71530.0561-0.1984-0.02910.1644-0.0704-0.1547-0.0650.09230.01430.0247-0.0132-0.02040.05080.00110.0451-35.01102.90614.024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 131
2X-RAY DIFFRACTION2A132 - 237
3X-RAY DIFFRACTION3A238 - 370
4X-RAY DIFFRACTION4B1 - 131
5X-RAY DIFFRACTION5B132 - 237
6X-RAY DIFFRACTION6B238 - 370

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