HEADER STRUCTURAL GENOMICS 27-AUG-23 8TZM TITLE SOLUTION STRUCTURE FOR A PUTATIVE TYPE I SITE-SPECIFIC TITLE 2 DEOXYRIBONUCLEASE FROM NEISSERIA GONORRHOEAE (NCCP11945). SEATTLE TITLE 3 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE TARGET TITLE 4 NEGOA.19201.A COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE I SITE-SPECIFIC DEOXYRIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 521006; SOURCE 4 STRAIN: NCCP11945; SOURCE 5 GENE: NGK_0701; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PUTATIVE DEOXYRIBONUCLEASE, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL KEYWDS 2 GENOMICS CENTER FOR INFECTIOUS DISEASE, SSGCID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.W.BUCHKO,SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE AUTHOR 2 (SSGCID) REVDAT 2 15-MAY-24 8TZM 1 REMARK REVDAT 1 04-OCT-23 8TZM 0 JRNL AUTH G.W.BUCHKO,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL STRUCTURAL CHARACTERIZATION OF A PUTATIVE TYPE I JRNL TITL 2 SITE-SPECIFIC DEOXYRIBONUCLEASE FROM NEISSERIA GONORRHOEAE JRNL TITL 3 (NCCP11945). JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL REMARK 3 OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE REMARK 3 FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED REMARK 3 MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) REMARK 3 AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE REMARK 3 RESTRAINTS AND THE VDW REMARK 4 REMARK 4 8TZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276977. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 N1, 100 MM SODIUM CHLORIDE, 20 REMARK 210 MM TRIS, 1 MM DTT, 93% H2O/7% REMARK 210 D2O; 0.8 MM [U-99% 15N] N1, 100 REMARK 210 MM SODIUM CHLORIDE, 20 MM TRIS, REMARK 210 1 MM DTT, 100% D2O; 0.5 MM [U-10% REMARK 210 13C; U-99% 15N] N1, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM TRIS, 1 REMARK 210 MM DTT, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-15N HSQC; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCA; 3D HCCH-TOCSY; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2017, CYANA 2.1, PSVS 1.5, REMARK 210 TALOS+, POKY 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA A 2 -60.54 73.47 REMARK 500 1 HIS A 5 109.18 -56.47 REMARK 500 1 PRO A 25 15.32 -67.46 REMARK 500 1 ASP A 83 69.37 60.29 REMARK 500 1 LYS A 94 16.76 51.64 REMARK 500 2 ALA A 2 -68.78 68.54 REMARK 500 2 HIS A 3 102.94 -58.84 REMARK 500 2 HIS A 6 33.81 -78.51 REMARK 500 2 HIS A 8 79.01 -69.13 REMARK 500 2 LYS A 38 90.16 -56.34 REMARK 500 2 HIS A 63 35.14 38.62 REMARK 500 2 LYS A 94 -72.31 66.45 REMARK 500 3 HIS A 6 122.84 -179.79 REMARK 500 3 ILE A 26 -75.28 -53.10 REMARK 500 3 LYS A 38 -179.45 -61.75 REMARK 500 3 LYS A 41 90.62 -61.26 REMARK 500 3 ASP A 83 73.70 60.80 REMARK 500 3 GLN A 95 -158.36 -156.19 REMARK 500 4 HIS A 7 143.08 -171.57 REMARK 500 4 HIS A 8 113.37 -164.34 REMARK 500 4 LEU A 11 -73.03 -86.17 REMARK 500 4 ASP A 28 99.56 -59.10 REMARK 500 4 ILE A 40 -87.47 -129.89 REMARK 500 4 LYS A 41 138.36 -174.30 REMARK 500 4 HIS A 63 36.76 37.51 REMARK 500 4 LYS A 94 -72.95 68.87 REMARK 500 5 ASP A 12 133.49 -170.83 REMARK 500 5 PRO A 25 8.91 -62.64 REMARK 500 5 ILE A 26 -71.88 -60.68 REMARK 500 5 HIS A 39 -90.18 63.17 REMARK 500 5 ILE A 40 -84.24 46.58 REMARK 500 5 LYS A 41 89.97 -169.04 REMARK 500 5 HIS A 63 36.28 38.74 REMARK 500 5 LYS A 94 24.08 45.52 REMARK 500 5 GLN A 95 -109.05 -170.78 REMARK 500 5 LYS A 96 145.66 -174.49 REMARK 500 5 PHE A 114 32.27 -99.49 REMARK 500 6 PRO A 25 12.10 -65.83 REMARK 500 6 LYS A 41 84.82 -61.89 REMARK 500 6 LYS A 94 -50.92 71.30 REMARK 500 7 ILE A 40 -66.49 -92.60 REMARK 500 7 LYS A 41 85.79 -172.45 REMARK 500 7 HIS A 63 38.73 38.15 REMARK 500 7 LYS A 94 -77.55 57.32 REMARK 500 8 ALA A 2 102.31 -52.77 REMARK 500 8 PRO A 25 7.78 -62.59 REMARK 500 8 LYS A 38 31.09 -77.51 REMARK 500 8 ILE A 40 -74.84 -104.77 REMARK 500 8 HIS A 63 36.18 36.99 REMARK 500 8 LYS A 94 -70.74 64.82 REMARK 500 REMARK 500 THIS ENTRY HAS 132 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31103 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE FOR A PUTATIVE TYPE I SITE-SPECIFIC REMARK 900 DEOXYRIBONUCLEASE FROM NEISSERIA GONORRHOEAE (NCCP11945). SEATTLE REMARK 900 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE TARGET REMARK 900 NEGOA.19201.A DBREF 8TZM A 9 115 UNP B4RKP1 B4RKP1_NEIG2 1 107 SEQADV 8TZM MET A 1 UNP B4RKP1 INITIATING METHIONINE SEQADV 8TZM ALA A 2 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 3 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 4 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 5 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 6 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 7 UNP B4RKP1 EXPRESSION TAG SEQADV 8TZM HIS A 8 UNP B4RKP1 EXPRESSION TAG SEQRES 1 A 115 MET ALA HIS HIS HIS HIS HIS HIS MET PHE LEU ASP ASP SEQRES 2 A 115 VAL ASN VAL PHE LEU ASP ASP LEU ASN THR ASN PRO ILE SEQRES 3 A 115 THR ASP GLU TRP TYR MET SER ASN PHE ALA ASP LYS HIS SEQRES 4 A 115 ILE LYS ILE LEU GLU SER TYR GLU ALA PHE ASP ILE LEU SEQRES 5 A 115 LYS GLN PHE VAL ASP TYR MET ILE GLU GLU HIS ASP GLU SEQRES 6 A 115 LYS SER GLU TYR GLU ILE MET GLU ILE LEU ARG GLN LEU SEQRES 7 A 115 LYS TYR GLN ALA ASP THR ASN GLU LYS PHE TYR THR ASN SEQRES 8 A 115 THR GLN LYS GLN LYS ILE VAL GLU LEU TYR LYS GLN GLU SEQRES 9 A 115 ILE SER GLN ASP ILE LEU ASN GLU ILE PHE ARG HELIX 1 AA1 ASP A 12 ASN A 24 1 13 HELIX 2 AA2 GLU A 29 ASP A 37 1 9 HELIX 3 AA3 GLU A 44 GLU A 61 1 18 HELIX 4 AA4 GLU A 62 HIS A 63 5 2 HELIX 5 AA5 ASP A 64 LYS A 66 5 3 HELIX 6 AA6 SER A 67 ASP A 83 1 17 HELIX 7 AA7 LYS A 96 LEU A 100 5 5 HELIX 8 AA8 LYS A 102 PHE A 114 1 13 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 MODEL 1