HEADER METAL BINDING PROTEIN 20-JAN-24 8XZ2 TITLE THE STRUCTURAL MODEL OF A HOMODIMERIC D-ALA-D-ALA METALLOPEPTIDASE, TITLE 2 VANX, FROM VANCOMYCIN-RESISTANT BACTERIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANYL-D-ALANINE DIPEPTIDASE; COMPND 3 CHAIN: B, C; COMPND 4 SYNONYM: D-ALA-D-ALA DIPEPTIDASE,VANCOMYCIN B-TYPE RESISTANCE PROTEIN COMPND 5 VANX; COMPND 6 EC: 3.4.13.22; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM; SOURCE 3 ORGANISM_TAXID: 1352; SOURCE 4 GENE: VANX; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS KEYWDS ACID-SELECTIVE UNLABELING, ANTIMICROBIAL RESISTANCE, HOMODIMER, KEYWDS 2 RESIDUAL DIPOLAR COUPLING (RDC), TRANSFER CROSS SATURATION (TCS), KEYWDS 3 VANCOMYCIN-RESISTANT ENTEROCOCCI, VANX, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR T.KONUMA,T.TAKAI,C.TSUCHIYA,M.NISHIDA,M.HASHIBA,Y.YAMADA,H.SHIRAI, AUTHOR 2 Y.MOTODA,A.NAGADOI,E.CHIKAISHI,K.AKAGI,S.AKASHI,T.YAMAZAKI,H.AKUTSU, AUTHOR 3 A.OE,T.IKEGAMI REVDAT 1 22-MAY-24 8XZ2 0 JRNL AUTH T.KONUMA,T.TAKAI,C.TSUCHIYA,M.NISHIDA,M.HASHIBA,Y.YAMADA, JRNL AUTH 2 H.SHIRAI,Y.MOTODA,A.NAGADOI,E.CHIKAISHI,K.I.AKAGI,S.AKASHI, JRNL AUTH 3 T.YAMAZAKI,H.AKUTSU,T.IKEGAMI JRNL TITL ANALYSIS OF THE HOMODIMERIC STRUCTURE OF A D-ALA-D-ALA JRNL TITL 2 METALLOPEPTIDASE, VANX, FROM VANCOMYCIN-RESISTANT BACTERIA. JRNL REF PROTEIN SCI. V. 33 E5002 2024 JRNL REFN ESSN 1469-896X JRNL PMID 38723146 JRNL DOI 10.1002/PRO.5002 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 2.4 REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN TOTAL, 132 RDC-BASED ORIENTATIONAL REMARK 3 RESTRAINTS AND SEVEN TCS-BASED INTERSUBUNIT AMBIGUOUS RESTRAINTS REMARK 3 WERE IMPOSED IN THE CALCULATIONS. THE LATTER RESTRAINTS INVOLVED REMARK 3 RESIDUES IN SEGMENTS B (SELECTED FROM RESIDUES EXHIBITING REMARK 3 REMARKABLE TCS EFFECTS) AND C (SELECTED FROM RESIDUES EXHIBITING REMARK 3 BOTH REMARKABLE AND MINOR TCS EFFECTS). THESE CONSTRAINTS WERE REMARK 3 APPLIED C2-SYMMETRICALLY BETWEEN THE SUBUNITS B AND C IN THE REMARK 3 CALCULATIONS. REMARK 4 REMARK 4 8XZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300043006. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.154 MM [U-13C; U-15N; U-2H] REMARK 210 VANX, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H/15N TROSY IPAP; TRANSFER REMARK 210 CROSS SATURATION REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PALES, NMRFAM-SPARKY, NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 H ALA B 57 H ALA B 58 1.26 REMARK 500 H ALA C 57 H ALA C 58 1.26 REMARK 500 HD21 ASN C 26 H THR C 28 1.26 REMARK 500 HD21 ASN B 26 H THR B 28 1.27 REMARK 500 HH22 ARG C 128 OD1 ASP C 130 1.49 REMARK 500 OD2 ASP B 9 HH21 ARG B 39 1.50 REMARK 500 OD2 ASP C 9 HH21 ARG C 39 1.51 REMARK 500 OE2 GLU B 133 HZ3 LYS C 30 1.53 REMARK 500 HZ2 LYS B 20 OD2 ASP B 25 1.54 REMARK 500 O GLY B 69 HD1 HIS B 116 1.57 REMARK 500 O GLY C 69 HD1 HIS C 116 1.57 REMARK 500 OE2 GLU B 10 HH22 ARG B 39 1.57 REMARK 500 O GLY C 61 H LEU C 129 1.58 REMARK 500 H THR C 6 O GLY C 42 1.58 REMARK 500 HH TYR B 21 OD2 ASP B 142 1.59 REMARK 500 HH TYR B 35 OD1 ASP B 68 1.59 REMARK 500 HH TYR C 21 OD2 ASP C 142 1.59 REMARK 500 HE ARG C 128 OD2 ASP C 130 1.59 REMARK 500 HZ2 LYS C 20 OD2 ASP C 25 1.60 REMARK 500 O GLY B 61 H LEU B 129 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 HIS B 13 -84.54 -37.49 REMARK 500 1 ARG B 16 68.85 -114.16 REMARK 500 1 ASP B 18 89.88 -161.37 REMARK 500 1 ALA B 19 83.83 -63.31 REMARK 500 1 ASP B 25 53.50 -94.71 REMARK 500 1 GLU B 36 -69.44 -97.52 REMARK 500 1 THR B 59 -146.03 -58.29 REMARK 500 1 TYR B 96 58.05 -156.05 REMARK 500 1 ASN B 98 -20.13 77.08 REMARK 500 1 ILE B 105 48.64 -98.97 REMARK 500 1 SER B 106 -40.71 -158.84 REMARK 500 1 ASN B 194 -15.62 76.54 REMARK 500 1 ASP B 198 29.95 -142.64 REMARK 500 1 HIS C 13 -87.74 -38.16 REMARK 500 1 ARG C 16 70.59 -114.00 REMARK 500 1 ASP C 18 91.96 -164.45 REMARK 500 1 ALA C 19 86.97 -63.03 REMARK 500 1 ASP C 25 52.98 -93.65 REMARK 500 1 VAL C 37 133.76 -170.12 REMARK 500 1 THR C 59 -146.13 -58.19 REMARK 500 1 TYR C 96 57.88 -156.08 REMARK 500 1 ASN C 98 -20.11 76.95 REMARK 500 1 ILE C 105 48.62 -98.97 REMARK 500 1 SER C 106 -40.82 -158.81 REMARK 500 1 ASN C 194 -15.60 76.37 REMARK 500 1 ASP C 198 29.82 -142.78 REMARK 500 2 HIS B 13 -85.57 -37.68 REMARK 500 2 ARG B 16 66.75 -114.70 REMARK 500 2 ASP B 18 90.73 -160.39 REMARK 500 2 ALA B 19 103.21 -57.72 REMARK 500 2 ASP B 25 52.51 -92.94 REMARK 500 2 VAL B 37 139.85 -170.77 REMARK 500 2 THR B 59 -143.03 -57.01 REMARK 500 2 TYR B 96 57.58 -154.52 REMARK 500 2 ASN B 98 -20.77 77.11 REMARK 500 2 ILE B 105 49.10 -99.43 REMARK 500 2 SER B 106 -40.94 -157.92 REMARK 500 2 ASN B 194 -16.88 78.45 REMARK 500 2 ASP B 198 30.26 -143.51 REMARK 500 2 HIS C 13 -83.95 -37.08 REMARK 500 2 ARG C 16 67.36 -116.19 REMARK 500 2 ASP C 18 87.94 -155.85 REMARK 500 2 ASP C 25 52.51 -93.37 REMARK 500 2 VAL C 37 139.73 -172.36 REMARK 500 2 THR C 59 -143.08 -57.05 REMARK 500 2 TYR C 96 57.73 -154.46 REMARK 500 2 ASN C 98 -20.70 77.10 REMARK 500 2 ILE C 105 49.04 -99.45 REMARK 500 2 SER C 106 -40.93 -157.86 REMARK 500 2 ASN C 194 -17.08 78.59 REMARK 500 REMARK 500 THIS ENTRY HAS 96 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 52158 RELATED DB: BMRB REMARK 900 RELATED ID: 1R44 RELATED DB: PDB REMARK 900 1R44 IS THE CRYSTAL STRUCTURE OF VANX CONSISTING OF THE SAME AMINO REMARK 900 ACID SEQUENCE, DETERMINED BY OTHER AUTHORS. DBREF 8XZ2 B 1 202 UNP Q06241 VANX_ENTFC 1 202 DBREF 8XZ2 C 1 202 UNP Q06241 VANX_ENTFC 1 202 SEQRES 1 B 202 MET GLU ILE GLY PHE THR PHE LEU ASP GLU ILE VAL HIS SEQRES 2 B 202 GLY VAL ARG TRP ASP ALA LYS TYR ALA THR TRP ASP ASN SEQRES 3 B 202 PHE THR GLY LYS PRO VAL ASP GLY TYR GLU VAL ASN ARG SEQRES 4 B 202 ILE VAL GLY THR TYR GLU LEU ALA GLU SER LEU LEU LYS SEQRES 5 B 202 ALA LYS GLU LEU ALA ALA THR GLN GLY TYR GLY LEU LEU SEQRES 6 B 202 LEU TRP ASP GLY TYR ARG PRO LYS ARG ALA VAL ASN CYS SEQRES 7 B 202 PHE MET GLN TRP ALA ALA GLN PRO GLU ASN ASN LEU THR SEQRES 8 B 202 LYS GLU SER TYR TYR PRO ASN ILE ASP ARG THR GLU MET SEQRES 9 B 202 ILE SER LYS GLY TYR VAL ALA SER LYS SER SER HIS SER SEQRES 10 B 202 ARG GLY SER ALA ILE ASP LEU THR LEU TYR ARG LEU ASP SEQRES 11 B 202 THR GLY GLU LEU VAL PRO MET GLY SER ARG PHE ASP PHE SEQRES 12 B 202 MET ASP GLU ARG SER HIS HIS ALA ALA ASN GLY ILE SER SEQRES 13 B 202 CYS ASN GLU ALA GLN ASN ARG ARG ARG LEU ARG SER ILE SEQRES 14 B 202 MET GLU ASN SER GLY PHE GLU ALA TYR SER LEU GLU TRP SEQRES 15 B 202 TRP HIS TYR VAL LEU ARG ASP GLU PRO TYR PRO ASN SER SEQRES 16 B 202 TYR PHE ASP PHE PRO VAL LYS SEQRES 1 C 202 MET GLU ILE GLY PHE THR PHE LEU ASP GLU ILE VAL HIS SEQRES 2 C 202 GLY VAL ARG TRP ASP ALA LYS TYR ALA THR TRP ASP ASN SEQRES 3 C 202 PHE THR GLY LYS PRO VAL ASP GLY TYR GLU VAL ASN ARG SEQRES 4 C 202 ILE VAL GLY THR TYR GLU LEU ALA GLU SER LEU LEU LYS SEQRES 5 C 202 ALA LYS GLU LEU ALA ALA THR GLN GLY TYR GLY LEU LEU SEQRES 6 C 202 LEU TRP ASP GLY TYR ARG PRO LYS ARG ALA VAL ASN CYS SEQRES 7 C 202 PHE MET GLN TRP ALA ALA GLN PRO GLU ASN ASN LEU THR SEQRES 8 C 202 LYS GLU SER TYR TYR PRO ASN ILE ASP ARG THR GLU MET SEQRES 9 C 202 ILE SER LYS GLY TYR VAL ALA SER LYS SER SER HIS SER SEQRES 10 C 202 ARG GLY SER ALA ILE ASP LEU THR LEU TYR ARG LEU ASP SEQRES 11 C 202 THR GLY GLU LEU VAL PRO MET GLY SER ARG PHE ASP PHE SEQRES 12 C 202 MET ASP GLU ARG SER HIS HIS ALA ALA ASN GLY ILE SER SEQRES 13 C 202 CYS ASN GLU ALA GLN ASN ARG ARG ARG LEU ARG SER ILE SEQRES 14 C 202 MET GLU ASN SER GLY PHE GLU ALA TYR SER LEU GLU TRP SEQRES 15 C 202 TRP HIS TYR VAL LEU ARG ASP GLU PRO TYR PRO ASN SER SEQRES 16 C 202 TYR PHE ASP PHE PRO VAL LYS HELIX 1 AA1 ASP B 9 ILE B 11 5 3 HELIX 2 AA2 ALA B 19 THR B 23 5 5 HELIX 3 AA3 TYR B 44 LEU B 56 1 13 HELIX 4 AA4 PRO B 72 ALA B 84 1 13 HELIX 5 AA5 THR B 91 TYR B 96 1 6 HELIX 6 AA6 SER B 114 GLY B 119 5 6 HELIX 7 AA7 ASP B 145 HIS B 149 5 5 HELIX 8 AA8 SER B 156 ASN B 172 1 17 HELIX 9 AA9 ASP C 9 ILE C 11 5 3 HELIX 10 AB1 ALA C 19 THR C 23 5 5 HELIX 11 AB2 TYR C 44 LEU C 56 1 13 HELIX 12 AB3 PRO C 72 ALA C 84 1 13 HELIX 13 AB4 THR C 91 TYR C 96 1 6 HELIX 14 AB5 SER C 114 GLY C 119 5 6 HELIX 15 AB6 ASP C 145 HIS C 149 5 5 HELIX 16 AB7 SER C 156 ASN C 172 1 17 SHEET 1 AA1 2 PHE B 5 PHE B 7 0 SHEET 2 AA1 2 VAL B 41 THR B 43 -1 O GLY B 42 N THR B 6 SHEET 1 AA2 4 TYR B 62 ASP B 68 0 SHEET 2 AA2 4 ALA B 121 ARG B 128 -1 O ASP B 123 N TRP B 67 SHEET 3 AA2 4 HIS B 184 LEU B 187 -1 O TYR B 185 N ILE B 122 SHEET 4 AA2 4 PHE B 175 ALA B 177 -1 N GLU B 176 O VAL B 186 SHEET 1 AA3 2 PHE C 5 PHE C 7 0 SHEET 2 AA3 2 VAL C 41 THR C 43 -1 O GLY C 42 N THR C 6 SHEET 1 AA4 4 TYR C 62 ASP C 68 0 SHEET 2 AA4 4 ALA C 121 ARG C 128 -1 O ASP C 123 N TRP C 67 SHEET 3 AA4 4 HIS C 184 LEU C 187 -1 O TYR C 185 N ILE C 122 SHEET 4 AA4 4 PHE C 175 ALA C 177 -1 N GLU C 176 O VAL C 186 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