PDB Short entry for 2KN9 HEADER ELECTRON TRANSPORT 20-AUG-09 2KN9 TITLE SOLUTION STRUCTURE OF ZINC-SUBSTITUTED RUBREDOXIN B (RV3250C) FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS. SEATTLE STRUCTURAL GENOMICS CENTER FOR TITLE 3 INFECTIOUS DISEASE TARGET MYTUD.01635.A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MT3348, RUBB, RV3250C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS TUBERCULOSIS, METALLOPROTEIN, RUBREDOXIN, SSGCID, STRUCTURAL KEYWDS 2 GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, KEYWDS 3 ELECTRON TRANSPORT, IRON, METAL-BINDING, TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.W.BUCHKO,S.N.HEWITT,A.J.NAPULI,W.C.VAN VOORHIS,SEATTLE STRUCTURAL AUTHOR 2 GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 3 01-MAY-24 2KN9 1 REMARK SEQADV REVDAT 2 21-SEP-11 2KN9 1 JRNL VERSN REVDAT 1 15-SEP-09 2KN9 0 JRNL AUTH G.W.BUCHKO,S.N.HEWITT,A.J.NAPULI,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL SOLUTION-STATE NMR STRUCTURE AND BIOPHYSICAL JRNL TITL 2 CHARACTERIZATION OF ZINC-SUBSTITUTED RUBREDOXIN B (RV3250C) JRNL TITL 3 FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 1148 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21904065 JRNL DOI 10.1107/S1744309111008189 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING CYANA (AUTO NOESYASSIGN). A TOTAL OF 20 REMARK 3 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL REMARK 3 SET OF CYANA CALCULATIONS WERE TAKEN AND REFINED BY RESTRAINED REMARK 3 MOLECULAR DYNAMICS IN EXPLICIT WATER (CNS). ZN-SG (2.20 - 2.40) REMARK 3 AND SG-SG (3.4 - 4.4) RESTRAINTS WERE ADDED ONLY TO THE FINAL REMARK 3 SET OF CYANA CALCULATIONS ON THE BASIS OF CALCULATIONS WITHOUT REMARK 3 THE RESTRAINTS AND OTHER PHYSICAL DATA. AT THE EXPLICIT WATER REMARK 3 REFINEMENT STAGE, 5% WAS ADDED TO THE UPPER BOUND RESTRAINT. REMARK 4 REMARK 4 2KN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000101331. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 0.12 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM SODIUM CHLORIDE, 1 MM REMARK 210 DTT, 20 MM TRIS, 1-2 MM [U-98% REMARK 210 13C; U-98% 15N] RV3250C, 90% H2O/ REMARK 210 10% D2O; 100 MM SODIUM CHLORIDE, REMARK 210 1 MM DTT, 20 MM TRIS, 1-2 MM [U- REMARK 210 98% 13C; U-98% 15N] RV3250C, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D REMARK 210 C(CO)NH; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; REMARK 210 DEUTERIUM EXCHANGE REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2007, SPARKY 3.115, PSVS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLN A 15 -73.15 -69.97 REMARK 500 1 CYS A 33 -40.89 -142.12 REMARK 500 1 CYS A 66 -11.09 -141.74 REMARK 500 1 ALA A 79 31.24 -92.59 REMARK 500 2 THR A 11 117.19 -161.05 REMARK 500 2 GLN A 15 -75.55 -65.34 REMARK 500 2 PRO A 19 -81.68 -77.15 REMARK 500 2 CYS A 33 -54.78 -149.95 REMARK 500 2 TRP A 43 78.99 -159.67 REMARK 500 2 CYS A 66 -81.25 -141.71 REMARK 500 3 ALA A 2 103.80 -59.41 REMARK 500 3 THR A 16 60.55 62.61 REMARK 500 3 GLN A 17 93.80 -67.75 REMARK 500 3 CYS A 33 -52.79 -152.20 REMARK 500 3 TRP A 43 85.55 -158.68 REMARK 500 4 GLN A 15 -75.27 -96.56 REMARK 500 4 CYS A 33 -56.84 -125.54 REMARK 500 4 TRP A 43 81.38 -157.18 REMARK 500 4 PRO A 64 48.03 -70.61 REMARK 500 4 ASP A 65 -51.87 -146.70 REMARK 500 5 SER A 21 92.86 -68.80 REMARK 500 5 CYS A 33 -42.80 -144.32 REMARK 500 5 TRP A 43 76.27 -150.11 REMARK 500 5 ALA A 79 108.60 -59.04 REMARK 500 6 HIS A 6 35.14 -84.65 REMARK 500 6 ASN A 23 -169.01 -116.52 REMARK 500 6 ASP A 24 21.99 -77.79 REMARK 500 6 CYS A 33 -56.40 -143.18 REMARK 500 6 TRP A 43 86.76 -153.35 REMARK 500 6 CYS A 66 -41.46 -155.76 REMARK 500 7 GLN A 15 -61.75 -101.44 REMARK 500 7 CYS A 33 -53.76 -150.77 REMARK 500 7 TRP A 43 82.87 -151.61 REMARK 500 7 PRO A 64 4.20 -66.77 REMARK 500 8 ALA A 2 97.93 70.03 REMARK 500 8 CYS A 33 -33.51 -153.07 REMARK 500 8 TRP A 43 85.96 -158.49 REMARK 500 8 CYS A 66 -50.43 -121.52 REMARK 500 9 ASN A 23 18.73 57.95 REMARK 500 9 CYS A 33 -56.45 -152.29 REMARK 500 9 TRP A 43 85.36 -151.16 REMARK 500 10 THR A 11 82.92 47.53 REMARK 500 10 MET A 22 -68.44 -109.13 REMARK 500 10 ASN A 23 71.86 -110.85 REMARK 500 10 ASP A 24 70.18 50.97 REMARK 500 10 CYS A 33 -50.72 -141.20 REMARK 500 11 LEU A 12 -167.08 -115.98 REMARK 500 11 CYS A 33 -57.44 -149.59 REMARK 500 11 CYS A 66 -53.85 -140.30 REMARK 500 12 HIS A 3 33.02 -147.23 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 82 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 30 SG REMARK 620 2 CYS A 33 SG 103.0 REMARK 620 3 CYS A 63 SG 119.3 120.0 REMARK 620 4 CYS A 66 SG 116.5 99.9 97.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 82 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16473 RELATED DB: BMRB REMARK 900 RELATED ID: MYTUD.01635.A RELATED DB: TARGETDB DBREF 2KN9 A 22 81 UNP O05893 O05893_MYCTU 1 60 SEQADV 2KN9 MET A 1 UNP O05893 EXPRESSION TAG SEQADV 2KN9 ALA A 2 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 3 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 4 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 5 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 6 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 7 UNP O05893 EXPRESSION TAG SEQADV 2KN9 HIS A 8 UNP O05893 EXPRESSION TAG SEQADV 2KN9 MET A 9 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLY A 10 UNP O05893 EXPRESSION TAG SEQADV 2KN9 THR A 11 UNP O05893 EXPRESSION TAG SEQADV 2KN9 LEU A 12 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLU A 13 UNP O05893 EXPRESSION TAG SEQADV 2KN9 ALA A 14 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLN A 15 UNP O05893 EXPRESSION TAG SEQADV 2KN9 THR A 16 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLN A 17 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLY A 18 UNP O05893 EXPRESSION TAG SEQADV 2KN9 PRO A 19 UNP O05893 EXPRESSION TAG SEQADV 2KN9 GLY A 20 UNP O05893 EXPRESSION TAG SEQADV 2KN9 SER A 21 UNP O05893 EXPRESSION TAG SEQRES 1 A 81 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 A 81 ALA GLN THR GLN GLY PRO GLY SER MET ASN ASP TYR LYS SEQRES 3 A 81 LEU PHE ARG CYS ILE GLN CYS GLY PHE GLU TYR ASP GLU SEQRES 4 A 81 ALA LEU GLY TRP PRO GLU ASP GLY ILE ALA ALA GLY THR SEQRES 5 A 81 ARG TRP ASP ASP ILE PRO ASP ASP TRP SER CYS PRO ASP SEQRES 6 A 81 CYS GLY ALA ALA LYS SER ASP PHE GLU MET VAL GLU VAL SEQRES 7 A 81 ALA ARG SER HET ZN A 82 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ALA A 69 SER A 71 5 3 SHEET 1 A 3 GLU A 36 ASP A 38 0 SHEET 2 A 3 LEU A 27 CYS A 30 -1 N PHE A 28 O TYR A 37 SHEET 3 A 3 PHE A 73 VAL A 76 -1 O VAL A 76 N LEU A 27 LINK SG CYS A 30 ZN ZN A 82 1555 1555 2.41 LINK SG CYS A 33 ZN ZN A 82 1555 1555 2.41 LINK SG CYS A 63 ZN ZN A 82 1555 1555 2.42 LINK SG CYS A 66 ZN ZN A 82 1555 1555 2.42 SITE 1 AC1 4 CYS A 30 CYS A 33 CYS A 63 CYS A 66 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000