HEADER HYDROLASE 16-OCT-09 2KPN TITLE SOLUTION NMR STRUCTURE OF A BACTERIAL IG-LIKE (BIG_3) DOMAIN FROM TITLE 2 BACILLUS CEREUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TITLE 3 BCR147A COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACILLOLYSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 658-753; COMPND 5 EC: 3.4.24.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS ATCC 14579; SOURCE 3 ORGANISM_TAXID: 226900; SOURCE 4 STRAIN: ATCC 14579 / DSM 31; SOURCE 5 GENE: BC_2506; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: BCR147A-658-751-21.1 KEYWDS SOLUTION NMR STRUCTURE, BIG_3 DOMAIN, PF07523, PSI BIG-OPEN TARGET, KEYWDS 2 NESG, CELL WALL, HYDROLASE, PEPTIDOGLYCAN-ANCHOR, STRUCTURAL KEYWDS 3 GENOMICS, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 4 GENOMICS CONSORTIUM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,D.WANG,C.T.CICCOSANTI,H.JANJUA,B.ROST,T.B.ACTON,R.XIAO, AUTHOR 2 G.V.T.SWAPNA,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 3 27-JUN-18 2KPN 1 SEQADV REVDAT 2 23-NOV-11 2KPN 1 VERSN ATOM REVDAT 1 12-JAN-10 2KPN 0 JRNL AUTH J.M.ARAMINI,D.WANG,C.T.CICCOSANTI,H.JANJUA,B.ROST,T.B.ACTON, JRNL AUTH 2 R.XIAO,G.V.T.SWAPNA,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF A BACTERIAL IG-LIKE (BIG_3) DOMAIN JRNL TITL 2 FROM BACILLUS CEREUS. NORTHEAST STRUCTURAL GENOMICS JRNL TITL 3 CONSORTIUM TARGET BCR147A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNS 1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1806 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 132 DIHEDRAL ANGLE CONSTRAINTS, AND 9 METAL-OXYGEN REMARK 3 DISTANCE CONSTRAINTS (20.8 CONSTRAINTS PER RESIDUE, 7.3 LONG REMARK 3 RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 97 BY REMARK 3 PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY REMARK 3 USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR REMARK 3 DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH REMARK 3 PARAM19. REMARK 4 REMARK 4 2KPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000101416. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.94 MM [U-100% 13C; U-100% 15N] REMARK 210 BCR147A, 20 MM MES, 200 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 50 UM DSS, 90% H2O/ REMARK 210 10% D2O; 0.78 MM [U-5% 13C; U- REMARK 210 100% 15N] BCR147A, 20 MM MES, REMARK 210 200 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC HIGH REMARK 210 RESOLUTION (L/V METHYL REMARK 210 STEREOASSIGNMENT); 2D 1H-15N REMARK 210 HETNOE; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 1D 1H- REMARK 210 15N T1 AND T2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, NMRPIPE 2.3, SPARKY REMARK 210 3.112, PINE 1.0, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.2.1, PSVS 1.3, REMARK 210 MOLPROBITY 3.15, PDBSTAT 5.1, REMARK 210 TALOS PLUS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, REMARK 210 STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE REMARK 210 WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA REMARK 210 FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7- REMARK 210 MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT REMARK 210 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE REMARK 210 USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING REMARK 210 CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOSPLUS. COMPLETENESS OF NMR ASSIGNMENTS REMARK 210 (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.5%, SIDE CHAIN, 99.2% REMARK 210 , AROMATICS, 100%, STEREOSPECIFIC METHYL, 90%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 66.7%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUE NUMBERS 1 TO 97, PSVS 1.3), WHERE ORDERED RESIDUES REMARK 210 [S(PHI) + S(PSI) > 1.8] COMPRISE: 7-85: (A) RMSD (ORDERED REMARK 210 RESIDUES): BB, 0.5, HEAVY ATOM, 0.8. (B) RAMACHANDRAN STATISTICS REMARK 210 FOR ORDERED RESIDUES: MOST FAVORED, 96.3%, ADDITIONALLY ALLOWED, REMARK 210 3.7%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK REMARK 210 SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.45/-1.46, ALL, REMARK 210 -0.27/-1.60. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.17/-0.91 (E) REMARK 210 RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-97): REMARK 210 RECALL, 0.979, PRECISION, 0.939, F-MEASURE, 0.959, DP-SCORE, REMARK 210 0.854. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 3. THE C- REMARK 210 TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT REMARK 210 INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED REMARK 210 FROM THIS DEPOSITION. THE LIGANDS INVOLVED IN THE CALCIUM ION REMARK 210 COORDINATION SPHERE ARE CONSISTENT WITH CHANGES IN THE NH-HSQC REMARK 210 SPECTRUM UPON REMOVAL/ADDITION OF CA2+. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 754 REMARK 465 HIS A 755 REMARK 465 HIS A 756 REMARK 465 HIS A 757 REMARK 465 HIS A 758 REMARK 465 HIS A 759 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 SER A 663 94.02 -65.67 REMARK 500 1 ASP A 748 45.96 -102.63 REMARK 500 1 LYS A 749 95.75 61.64 REMARK 500 1 PRO A 750 100.61 -55.75 REMARK 500 2 ASP A 681 -165.09 -78.01 REMARK 500 2 PRO A 750 73.47 -68.05 REMARK 500 3 GLU A 743 89.04 -69.63 REMARK 500 3 LYS A 746 86.31 -63.89 REMARK 500 4 ARG A 742 -80.39 -88.51 REMARK 500 4 LYS A 749 74.38 -167.91 REMARK 500 5 ARG A 742 -33.35 -145.96 REMARK 500 5 LYS A 749 94.11 -172.96 REMARK 500 6 LYS A 746 -71.41 -140.70 REMARK 500 6 LYS A 749 84.64 46.85 REMARK 500 6 LEU A 752 -21.03 -147.24 REMARK 500 7 ASN A 659 -168.94 -117.35 REMARK 500 7 GLU A 661 86.21 64.19 REMARK 500 7 VAL A 745 99.09 -69.82 REMARK 500 7 ASP A 748 -9.80 72.15 REMARK 500 8 ASP A 748 102.30 -53.26 REMARK 500 8 ILE A 751 88.37 -65.56 REMARK 500 9 THR A 662 88.15 61.27 REMARK 500 9 PRO A 750 97.78 -65.37 REMARK 500 11 ASP A 681 -161.94 -101.25 REMARK 500 11 ASP A 748 83.48 -67.66 REMARK 500 11 ILE A 751 24.39 -77.34 REMARK 500 12 LYS A 746 90.40 -61.95 REMARK 500 12 ASP A 748 32.24 -83.23 REMARK 500 12 LYS A 749 73.74 54.87 REMARK 500 13 ILE A 751 86.00 59.67 REMARK 500 13 LEU A 752 146.83 -177.57 REMARK 500 14 GLU A 661 -11.46 70.16 REMARK 500 14 GLU A 743 36.00 -77.83 REMARK 500 14 ASP A 748 35.42 -77.86 REMARK 500 14 LYS A 749 149.70 65.93 REMARK 500 14 ILE A 751 93.37 -64.18 REMARK 500 15 ASP A 681 -168.43 -75.62 REMARK 500 15 PRO A 750 -164.83 -78.24 REMARK 500 15 LEU A 752 99.86 -66.64 REMARK 500 16 ASN A 659 -65.41 -151.91 REMARK 500 16 GLU A 661 -71.01 -135.22 REMARK 500 16 THR A 662 88.51 61.21 REMARK 500 16 LYS A 749 143.20 65.38 REMARK 500 16 PRO A 750 92.04 -59.67 REMARK 500 17 LYS A 746 95.88 -67.06 REMARK 500 17 PRO A 750 109.13 -55.60 REMARK 500 17 ILE A 751 96.39 60.31 REMARK 500 18 PRO A 750 100.56 -51.80 REMARK 500 19 ASP A 748 38.98 -76.99 REMARK 500 19 LYS A 749 98.81 61.75 REMARK 500 REMARK 500 THIS ENTRY HAS 57 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 CA A 762 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 695 OE1 REMARK 620 2 ASP A 725 OD2 158.7 REMARK 620 3 ASP A 693 OD1 100.5 86.4 REMARK 620 4 ASP A 664 OD2 80.2 89.9 170.8 REMARK 620 5 ASP A 664 OD1 108.4 80.0 133.0 54.2 REMARK 620 6 ASP A 693 OD2 76.1 92.0 54.8 117.0 167.7 REMARK 620 7 LEU A 665 O 87.5 113.8 72.0 117.2 73.1 119.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 762 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BCR147A RELATED DB: TARGETDB REMARK 900 RELATED ID: 16561 RELATED DB: BMRB DBREF 2KPN A 658 752 UNP Q81D73 Q81D73_BACCR 658 752 SEQADV 2KPN MET A 657 UNP Q81D73 INITIATING METHIONINE SEQADV 2KPN GLU A 753 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 754 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 755 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 756 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 757 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 758 UNP Q81D73 EXPRESSION TAG SEQADV 2KPN HIS A 759 UNP Q81D73 EXPRESSION TAG SEQRES 1 A 103 MET GLY ASN GLY GLU THR SER ASP LEU GLU PRO LYS LEU SEQRES 2 A 103 THR VAL PRO VAL GLY ALA THR ILE HIS VAL GLY ASP SER SEQRES 3 A 103 PHE VAL PRO MET ALA GLU VAL LEU ALA ILE ASP LYS GLU SEQRES 4 A 103 ASP GLY ASP LEU THR SER LYS ILE LYS VAL ASP GLY GLU SEQRES 5 A 103 VAL ASP THR THR LYS ALA GLY THR TYR VAL LEU THR TYR SEQRES 6 A 103 THR VAL THR ASP SER LYS GLY HIS GLU VAL THR ALA LYS SEQRES 7 A 103 GLN THR VAL THR VAL LYS VAL ARG GLU GLU VAL LYS ASN SEQRES 8 A 103 ASP LYS PRO ILE LEU GLU HIS HIS HIS HIS HIS HIS HET CA A 762 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 VAL A 684 VAL A 689 1 6 HELIX 2 2 LEU A 699 ILE A 703 5 5 SHEET 1 A 2 LYS A 668 THR A 670 0 SHEET 2 A 2 LEU A 690 ILE A 692 -1 O LEU A 690 N THR A 670 SHEET 1 B 4 GLY A 674 HIS A 678 0 SHEET 2 B 4 GLU A 730 LYS A 740 1 O THR A 736 N ALA A 675 SHEET 3 B 4 GLY A 715 THR A 724 -1 N TYR A 721 O ALA A 733 SHEET 4 B 4 LYS A 704 ASP A 706 -1 N ASP A 706 O THR A 720 LINK OE1 GLU A 695 CA CA A 762 1555 1555 2.17 LINK OD2 ASP A 725 CA CA A 762 1555 1555 2.29 LINK OD1 ASP A 693 CA CA A 762 1555 1555 2.33 LINK OD2 ASP A 664 CA CA A 762 1555 1555 2.37 LINK OD1 ASP A 664 CA CA A 762 1555 1555 2.38 LINK OD2 ASP A 693 CA CA A 762 1555 1555 2.39 LINK O LEU A 665 CA CA A 762 1555 1555 2.44 SITE 1 AC1 5 ASP A 664 LEU A 665 ASP A 693 GLU A 695 SITE 2 AC1 5 ASP A 725 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