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- PDB-3fwy: Crystal structure of the L protein of Rhodobacter sphaeroides lig... -

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Basic information

Entry
Database: PDB / ID: 3fwy
TitleCrystal structure of the L protein of Rhodobacter sphaeroides light-independent protochlorophyllide reductase (BchL) with MgADP bound: a homologue of the nitrogenase Fe protein
ComponentsLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
KeywordsOXIDOREDUCTASE / BchL / protochlorophyllide / Electron donor / DPOR / Fe protein / nitrogenase / mixed alpha-beta domain / MgADP / ATP-binding / Bacteriochlorophyll biosynthesis / Chlorophyll biosynthesis / Iron / Iron-sulfur / Metal-binding / Nucleotide-binding / Photosynthesis
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Light-independent protochlorophyllide reductase, iron-sulphur ATP-binding protein / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSarma, R. / Barney, B.M. / Hamilton, T.L. / Jones, A. / Seefeldt, L.C. / Peters, J.W.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal Structure of the L Protein of Rhodobacter sphaeroides Light-Independent Protochlorophyllide Reductase with MgADP Bound: A Homologue of the Nitrogenase Fe Protein.
Authors: Sarma, R. / Barney, B.M. / Hamilton, T.L. / Jones, A. / Seefeldt, L.C. / Peters, J.W.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionMar 24, 2009ID: 3END
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
B: Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2857
Polymers69,0302
Non-polymers1,2555
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-10.6 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.729, 86.622, 117.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 30 - 250 / Label seq-ID: 47 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Light-independent protochlorophyllide reductase iron-sulfur ATP-binding protein / LI-POR subunit L / DPOR subunit L


Mass: 34515.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: 2.4.1 / NCIB 8253 / DSM 158 / Gene: bchL, RHOS4_18930, RSP_0288 / Plasmid: pUC / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: Q9RFD6, EC: 1.18.-.-
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 301 K / Method: capillary batch diffusion / pH: 7.8
Details: 20-25% PEG 3350, 200mM Magnesium formate, 10mM MgADP, pH 7.8, CAPILLARY BATCH DIFFUSION, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 19, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 133747 / Num. obs: 133747 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.037 / Net I/σ(I): 40
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 2 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 13313 / Rsym value: 0.242 / % possible all: 93.83

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NIP

2nip


Resolution: 1.63→33.02 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.339 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.63 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 3544 5 %RANDOM
Rwork0.17403 ---
obs0.17529 66727 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.63→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 64 402 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224333
X-RAY DIFFRACTIONr_bond_other_d0.0010.022915
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9845898
X-RAY DIFFRACTIONr_angle_other_deg0.87437101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4623.776196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91415716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8121532
X-RAY DIFFRACTIONr_chiral_restr0.1520.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined0.2170.2927
X-RAY DIFFRACTIONr_nbd_other0.190.23092
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22161
X-RAY DIFFRACTIONr_nbtor_other0.0820.22206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2283
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.223
X-RAY DIFFRACTIONr_mcbond_it1.43423449
X-RAY DIFFRACTIONr_mcbond_other0.51221105
X-RAY DIFFRACTIONr_mcangle_it1.75834328
X-RAY DIFFRACTIONr_scbond_it4.59591884
X-RAY DIFFRACTIONr_scangle_it6.086121549
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2773 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.550.5
medium thermal0.812
LS refinement shellResolution: 1.63→1.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 235 -
Rwork0.168 4776 -
obs--93.86 %
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)
10.57720.07890.00511.285-0.19260.9499-0.03030.0405-0.104-0.11360.036-0.0250.2216-0.075-0.00570.0808-0.01110.00180.0637-0.00460.11352.863646.023961.0448
26.76372.67111.2352.7107-0.18572.5367-0.26670.1396-0.4988-0.37860.0317-0.66830.22040.31580.2350.11180.05650.08760.0778-0.00120.29419.421842.201157.4529
31.83821.1512-0.49542.151-0.47580.1527-0.06460.019-0.1352-0.01750.0476-0.20180.19240.07610.0170.08060.02660.01570.08820.00080.157215.017149.68460.8295
438.2142.723511.51944.09181.89393.7678-0.01212.12080.0469-0.37690.17260.073-0.2030.1725-0.16050.2737-0.09080.05260.3729-0.02550.14959.742848.990246.8863
50.80130.1495-0.07190.6771-0.12670.65770.0093-0.00840.01050.03120.02160.01080.0807-0.0204-0.0310.044-0.0068-0.00370.08440.01020.11051.563959.914264.6412
62.39510.6872-0.60692.3461-1.39831.54780.03520.09370.11530.08630.13780.1408-0.0139-0.1421-0.17310.0485-0.0002-0.01110.0824-0.00470.1046-4.07260.061562.2554
71.612-0.8601-0.11182.9205-0.68361.3094-0.0566-0.1789-0.0710.1930.08490.32150.0046-0.2147-0.02840.0055-0.01820.0060.11470.03130.1154-13.605959.007168.0391
89.179-4.25452.762611.3072-3.12633.5061-0.3151-0.3244-0.29560.39770.48150.70330.3954-0.1052-0.16640.1232-0.03870.0378-0.0280.05790.0889-5.652936.437267.3103
93.00790.1453-2.146113.9117-3.15362.2003-0.2233-0.4192-0.3684-0.36530.70380.66161.0991-1.2789-0.48050.2873-0.2635-0.05830.39710.0770.236-14.465636.5162.8358
102.1679-0.98050.40973.5495-1.92923.25780.07230.0145-0.0928-0.21570.00570.20790.0969-0.4274-0.0780.0764-0.0405-0.03970.1447-0.03360.1229-11.069850.602653.9097
111.18880.25191.8120.43510.13053.0895-0.1251-0.21850.18340.0833-0.04030.1111-0.1332-0.24650.16530.04730.02260.01480.1385-0.02320.1359-7.329869.687770.8342
120.7111-0.9027-0.7251.78361.02071.7945-0.0137-0.0390.00410.3776-0.05980.00530.1655-0.0320.07350.1666-0.0352-0.00930.0999-0.01010.10176.527366.192590.7947
135.05161.1153-2.46577.4986-1.394713.86940.3270.14080.2811-0.3461-0.1588-0.489-0.61320.7204-0.16820.13310.01570.13610.0320.03430.189613.490583.59578.2439
140.5155-0.2425-0.66040.74080.91033.78050.0927-0.0850.13260.15530.0319-0.1498-0.25870.1595-0.12460.1464-0.0179-0.01170.0924-0.0140.15211.385274.138584.6373
151.14322.9026-4.86237.3746-12.305820.9741-0.0341-0.50150.2620.7238-0.1694-0.6119-0.5211.08530.20350.2479-0.0219-0.09990.3346-0.08770.321319.328173.396195.9051
160.3581-0.17380.32251.39070.91351.1670.0035-0.082900.3206-0.0706-0.0880.27690.0860.06710.18030.0059-0.0180.12520.01080.14412.292456.252184.2826
170.6512-0.01440.54612.11951.35791.9917-0.04240.054-0.01220.33530.1941-0.46790.35760.5384-0.15170.24830.0618-0.0730.25010.00480.253921.726954.091285.257
180.8487-0.9808-0.18182.12490.66770.3216-0.0305-0.1568-0.32930.546-0.1210.24950.28630.07840.15150.3693-0.0370.05870.13620.02690.22116.426144.715191.7624
195.09620.20711.02317.5324-2.87488.9086-0.1259-0.1438-0.38110.485-0.04760.68420.4985-0.57710.17350.1452-0.10780.15660.1194-0.08650.181-7.623461.725494.0036
207.4956-2.68161.73953.3769-0.96325.8692-0.1087-0.4282-0.23120.8691-0.19050.56520.5247-1.05370.29920.5388-0.15680.19870.2905-0.08730.1697-4.414658.6351103.484
210.45060.4365-0.40134.46442.40792.2926-0.0167-0.2733-0.08181.45990.1002-0.42880.74910.4722-0.08350.6220.0752-0.11660.13830.0460.070514.005854.3735101.8801
223.16711.13080.72983.8657-0.27091.30260.0864-0.1519-0.11640.4184-0.0942-0.26450.23130.02380.00780.19470.0305-0.01690.04230.03910.13812.427139.683678.5713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 88
2X-RAY DIFFRACTION2A89 - 109
3X-RAY DIFFRACTION3A110 - 141
4X-RAY DIFFRACTION4A142 - 147
5X-RAY DIFFRACTION5A148 - 198
6X-RAY DIFFRACTION6A199 - 215
7X-RAY DIFFRACTION7A216 - 238
8X-RAY DIFFRACTION8A239 - 252
9X-RAY DIFFRACTION9A253 - 264
10X-RAY DIFFRACTION10A265 - 276
11X-RAY DIFFRACTION11A277 - 297
12X-RAY DIFFRACTION12B30 - 88
13X-RAY DIFFRACTION13B89 - 100
14X-RAY DIFFRACTION14B101 - 141
15X-RAY DIFFRACTION15B142 - 148
16X-RAY DIFFRACTION16B149 - 188
17X-RAY DIFFRACTION17B189 - 208
18X-RAY DIFFRACTION18B209 - 236
19X-RAY DIFFRACTION19B237 - 250
20X-RAY DIFFRACTION20B251 - 265
21X-RAY DIFFRACTION21B266 - 280
22X-RAY DIFFRACTION22B281 - 297

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