HEADER HYDROLASE 15-JUL-16 5KVP TITLE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF ZOOCIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZOOCIN A ENDOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS EQUI SUBSP. ZOOEPIDEMICUS; SOURCE 3 ORGANISM_TAXID: 40041; SOURCE 4 GENE: ZOOA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, EXOENZYME, ANTI-MICROBIAL, ENDOPEPTIDASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.TIMKOVICH,M.XING,R.S.SIMMONDS REVDAT 3 26-JUL-17 5KVP 1 COMPND REMARK REVDAT 2 28-DEC-16 5KVP 1 JRNL REVDAT 1 26-OCT-16 5KVP 0 JRNL AUTH M.XING,R.S.SIMMONDS,R.TIMKOVICH JRNL TITL SOLUTION STRUCTURE OF THE CYS74 TO ALA74 MUTANT OF THE JRNL TITL 2 RECOMBINANT CATALYTIC DOMAIN OF ZOOCIN A. JRNL REF PROTEINS V. 85 177 2017 JRNL REFN ESSN 1097-0134 JRNL PMID 27699884 JRNL DOI 10.1002/PROT.25178 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222284. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297; 297; 297 REMARK 210 PH : 5.6; 5.6; 5.6 REMARK 210 IONIC STRENGTH : 0.02; 0.02; 0.02 REMARK 210 PRESSURE : 1.0 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM POTASSIUM PHOSPHATE, 0.1 REMARK 210 MM SODIUM AZIDE, 1.1 MM [U-95% REMARK 210 13C; U-90% 15N] PROTEIN, 95% H2O/ REMARK 210 5% D2O; 10 MM POTASSIUM REMARK 210 PHOSPHATE, 0.1 MM SODIUM AZIDE, REMARK 210 0.5 MM [U-95% 13C; U-90% 15N] REMARK 210 PROTEIN, 95% H2O/5% D2O; 10 MM REMARK 210 POTASSIUM PHOSPHATE, 0.1 MM REMARK 210 SODIUM AZIDE, 1.0 MM [U-90% 15N] REMARK 210 PROTEIN, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 3D HN(CO)CA; 3D REMARK 210 HN(CA)CO; 3D HCCH-TOCSY; 3D HNHA; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D CCC-TOCSY; 3D HCC-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3, NMRVIEW, NMRPIPE, REMARK 210 NMRDRAW, TALOS+, TOPSPIN 1.2, REMARK 210 DEEPVIEW/SWISS-PDB VIEWER, REMARK 210 PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 O ALA A 49 H GLY A 104 1.50 REMARK 500 O PHE A 28 H GLY A 30 1.60 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 THR A 21 -168.83 -168.77 REMARK 500 1 ILE A 24 58.19 -102.97 REMARK 500 1 ASN A 29 32.04 -56.94 REMARK 500 1 ALA A 40 104.83 -58.68 REMARK 500 1 ALA A 51 143.74 -171.44 REMARK 500 1 MET A 70 -28.22 -144.52 REMARK 500 1 HIS A 79 -176.09 -68.31 REMARK 500 1 ASP A 98 -5.18 86.43 REMARK 500 1 ALA A 112 48.16 -150.33 REMARK 500 1 THR A 117 -52.98 -146.78 REMARK 500 1 PRO A 127 -178.43 -64.09 REMARK 500 1 ASN A 131 70.76 -117.96 REMARK 500 1 TRP A 132 13.67 -62.90 REMARK 500 1 GLN A 133 33.72 -81.81 REMARK 500 1 ASN A 134 128.20 71.95 REMARK 500 1 PHE A 136 -19.58 -150.78 REMARK 500 1 PRO A 150 178.56 -54.93 REMARK 500 1 ASN A 153 -37.83 68.52 REMARK 500 1 THR A 158 -62.61 -163.26 REMARK 500 2 ALA A 13 108.26 -160.17 REMARK 500 2 THR A 21 -168.94 -168.21 REMARK 500 2 ILE A 24 58.31 -102.56 REMARK 500 2 ASN A 29 31.92 -55.70 REMARK 500 2 ALA A 51 144.17 -171.55 REMARK 500 2 MET A 70 -36.88 -145.68 REMARK 500 2 HIS A 79 -177.93 -69.99 REMARK 500 2 ASP A 98 -4.97 87.47 REMARK 500 2 ALA A 112 52.94 -150.30 REMARK 500 2 HIS A 120 -166.69 -160.72 REMARK 500 2 PRO A 127 -178.57 -63.16 REMARK 500 2 ASN A 131 69.62 -117.50 REMARK 500 2 TRP A 132 12.30 -62.19 REMARK 500 2 GLN A 133 33.15 -81.76 REMARK 500 2 ASN A 134 128.79 73.11 REMARK 500 2 PHE A 136 -18.96 -152.21 REMARK 500 2 PRO A 150 178.77 -54.89 REMARK 500 2 ASN A 153 -38.58 69.32 REMARK 500 2 THR A 158 -66.42 -163.11 REMARK 500 3 THR A 21 -168.84 -169.39 REMARK 500 3 ILE A 24 58.58 -102.99 REMARK 500 3 ASN A 29 31.89 -57.86 REMARK 500 3 ALA A 40 104.26 -57.86 REMARK 500 3 ALA A 51 144.46 -171.46 REMARK 500 3 MET A 70 -31.02 -145.56 REMARK 500 3 HIS A 79 -175.85 -69.17 REMARK 500 3 ASP A 98 -5.71 86.96 REMARK 500 3 ALA A 112 50.78 -150.10 REMARK 500 3 PRO A 127 -178.68 -63.62 REMARK 500 3 ASN A 131 70.33 -117.23 REMARK 500 3 TRP A 132 13.67 -63.25 REMARK 500 REMARK 500 THIS ENTRY HAS 188 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE OXYGEN ATOM IN UNL LIGAND COMES FROM WATER OR PHOSPHATE IONS IN REMARK 600 THE BUFFER 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 34 NE2 REMARK 620 2 ASP A 38 OD1 105.0 REMARK 620 3 ASP A 38 OD2 70.5 58.1 REMARK 620 4 HIS A 122 ND1 104.8 104.9 158.3 REMARK 620 5 UNL A 202 O 106.2 125.7 92.9 108.6 REMARK 620 N 1 2 3 4 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30139 RELATED DB: BMRB DBREF 5KVP A 13 159 UNP O54308 O54308_STRSZ 24 170 SEQADV 5KVP MET A 1 UNP O54308 EXPRESSION TAG SEQADV 5KVP ARG A 2 UNP O54308 EXPRESSION TAG SEQADV 5KVP GLY A 3 UNP O54308 EXPRESSION TAG SEQADV 5KVP SER A 4 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 5 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 6 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 7 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 8 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 9 UNP O54308 EXPRESSION TAG SEQADV 5KVP HIS A 10 UNP O54308 EXPRESSION TAG SEQADV 5KVP GLY A 11 UNP O54308 EXPRESSION TAG SEQADV 5KVP SER A 12 UNP O54308 EXPRESSION TAG SEQADV 5KVP ALA A 74 UNP O54308 CYS 85 ENGINEERED MUTATION SEQRES 1 A 159 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 A 159 THR TYR THR ARG PRO LEU ASP THR GLY ASN ILE THR THR SEQRES 3 A 159 GLY PHE ASN GLY TYR PRO GLY HIS VAL GLY VAL ASP TYR SEQRES 4 A 159 ALA VAL PRO VAL GLY THR PRO VAL ARG ALA VAL ALA ASN SEQRES 5 A 159 GLY THR VAL LYS PHE ALA GLY ASN GLY ALA ASN HIS PRO SEQRES 6 A 159 TRP MET LEU TRP MET ALA GLY ASN ALA VAL LEU ILE GLN SEQRES 7 A 159 HIS ALA ASP GLY MET HIS THR GLY TYR ALA HIS LEU SER SEQRES 8 A 159 LYS ILE SER VAL SER THR ASP SER THR VAL LYS GLN GLY SEQRES 9 A 159 GLN ILE ILE GLY TYR THR GLY ALA THR GLY GLN VAL THR SEQRES 10 A 159 GLY PRO HIS LEU HIS PHE GLU MET LEU PRO ALA ASN PRO SEQRES 11 A 159 ASN TRP GLN ASN GLY PHE SER GLY ARG ILE ASP PRO THR SEQRES 12 A 159 GLY TYR ILE ALA ASN ALA PRO VAL PHE ASN GLY THR THR SEQRES 13 A 159 PRO THR GLU HET ZN A 201 1 HET UNL A 202 1 HETNAM ZN ZINC ION HETNAM UNL UNKNOWN LIGAND FORMUL 2 ZN ZN 2+ HELIX 1 AA1 PRO A 142 ALA A 147 1 6 SHEET 1 AA1 5 VAL A 37 ALA A 40 0 SHEET 2 AA1 5 HIS A 120 LEU A 126 -1 O PHE A 123 N VAL A 37 SHEET 3 AA1 5 HIS A 84 ILE A 93 -1 N GLY A 86 O GLU A 124 SHEET 4 AA1 5 ILE A 106 THR A 110 -1 O TYR A 109 N SER A 91 SHEET 5 AA1 5 PRO A 46 ARG A 48 -1 N VAL A 47 O GLY A 108 SHEET 1 AA2 6 VAL A 37 ALA A 40 0 SHEET 2 AA2 6 HIS A 120 LEU A 126 -1 O PHE A 123 N VAL A 37 SHEET 3 AA2 6 HIS A 84 ILE A 93 -1 N GLY A 86 O GLU A 124 SHEET 4 AA2 6 ASN A 73 GLN A 78 -1 N ILE A 77 O THR A 85 SHEET 5 AA2 6 GLY A 53 GLY A 59 -1 N GLY A 59 O ALA A 74 SHEET 6 AA2 6 THR A 100 VAL A 101 -1 O VAL A 101 N GLY A 53 LINK NE2 HIS A 34 ZN ZN A 201 1555 1555 2.04 LINK OD1 ASP A 38 ZN ZN A 201 1555 1555 2.01 LINK OD2 ASP A 38 ZN ZN A 201 1555 1555 2.45 LINK ND1 HIS A 122 ZN ZN A 201 1555 1555 2.05 LINK ZN ZN A 201 O UNL A 202 1555 1555 2.05 SITE 1 AC1 3 HIS A 34 ASP A 38 HIS A 122 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 187 0 2 1 11 0 1 6 0 0 0 13 END