PDB Short entry for 2AIZ HEADER MEMBRANE PROTEIN 01-AUG-05 2AIZ TITLE SOLUTION STRUCTURE OF PEPTIDOGLYCAN ASSOCIATED LIPOPROTEIN FROM TITLE 2 HAEMOPHILUS INFLUENZA BOUND TO UDP-N-ACETYLMURAMOYL-L-ALANYL-D- TITLE 3 GLUTAMYL-MESO-2,6-DIAMINOPIMELOYL-D-ALANYL-D-ALANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN P6 (FRAGMENT); COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: L-ALANYL-D-GLUTAMYL-MESO-2,6-DIAMINOPIMELOYL-D-ALANYL-D- COMPND 7 ALANINE; COMPND 8 CHAIN: U; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: OMPP6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS ALPHA-BETA SANDWICH, STRUCTURE 2 FUNCTION PROJECT, S2F, STRUCTURAL KEYWDS 2 GENOMICS, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.M.PARSONS,F.LIN,J.ORBAN,STRUCTURE 2 FUNCTION PROJECT (S2F) REVDAT 4 15-FEB-23 2AIZ 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQRES HETSYN LINK ATOM REVDAT 3 29-JUL-20 2AIZ 1 REMARK HETNAM LINK REVDAT 2 24-FEB-09 2AIZ 1 VERSN REVDAT 1 14-MAR-06 2AIZ 0 JRNL AUTH L.M.PARSONS,F.LIN,J.ORBAN JRNL TITL PEPTIDOGLYCAN RECOGNITION BY PAL, AN OUTER MEMBRANE JRNL TITL 2 LIPOPROTEIN. JRNL REF BIOCHEMISTRY V. 45 2122 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16475801 JRNL DOI 10.1021/BI052227I REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : REMARK 3 A.T.BRUNGER,P.D.ADAMS,G.M.CLORE,W.L.DELANO,P.GROS,R.W.GROSSE- REMARK 3 KUNSTLEVE,J.-S.JIANG,J.KUSZEWSKI,M.NILGES,N.S.PANNU,R.J.READ, REMARK 3 L.M.RICE,T.SIMONSON,G.L.WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AIZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033948. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298; 298 REMARK 210 PH : 6.7; 6.7; 6.7; 6.7; 6.7 REMARK 210 IONIC STRENGTH : 50MM PHOSPHATE, 50MM NACL; 50MM REMARK 210 PHOSPHATE, 50MM NACL; 50MM REMARK 210 PHOSPHATE, 50MM NACL; 50MM REMARK 210 PHOSPHATE, 50MM NACL; 50MM REMARK 210 PHOSPHATE, 50MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM PAL + UYP; 15N/13C. 50MM REMARK 210 PHOSPHATE 50MM NACL, PH6.7, 90% REMARK 210 H2O, 10% D2O; 0.8MM PAL + UYP; REMARK 210 15N/13C. 50MM PHOSPHATE 50MM REMARK 210 NACL, PH6.7, 100% D2O; 0.8MM REMARK 210 PAL(UNLABELED) + UYP(15N/13C). REMARK 210 50MM PHOSPHATE 50MM NACL, PH6.7, REMARK 210 100% D2O; 0.8MM PAL + UYP; 15N/ REMARK 210 13C. 50MM PHOSPHATE 50MM NACL, REMARK 210 PH6.7, PHAGE, 90% H2O 10% D2O; REMARK 210 1MM UYP 15N/13C, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 2.4, NMRPIPE 1.0 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: P, U 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: 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 P 2 163.26 58.70 REMARK 500 1 ALA P 8 17.95 -143.24 REMARK 500 1 ALA P 9 -17.75 81.94 REMARK 500 1 ALA P 14 142.61 -30.53 REMARK 500 1 ASN P 30 18.02 -160.77 REMARK 500 1 ASN P 79 -75.45 -67.66 REMARK 500 1 ILE P 80 -43.46 -29.70 REMARK 500 1 GLU P 112 -70.24 -47.65 REMARK 500 1 ALA P 115 -74.75 -97.68 REMARK 500 1 GLU P 121 -30.94 -38.44 REMARK 500 1 ARG P 128 83.22 -69.64 REMARK 500 1 LEU P 132 102.13 -59.19 REMARK 500 2 SER P 3 -173.54 -61.14 REMARK 500 2 ALA P 8 -88.24 -174.57 REMARK 500 2 ALA P 9 -55.96 69.81 REMARK 500 2 ASN P 11 135.19 66.20 REMARK 500 2 ALA P 13 -72.48 -46.21 REMARK 500 2 ALA P 14 69.38 61.74 REMARK 500 2 GLN P 15 -109.57 -118.66 REMARK 500 2 ASN P 30 22.65 179.66 REMARK 500 2 ASP P 37 26.00 49.67 REMARK 500 2 ARG P 73 108.95 -39.59 REMARK 500 2 ASN P 79 -76.85 -70.51 REMARK 500 2 VAL P 107 129.22 -171.13 REMARK 500 2 ALA P 115 -62.70 -107.38 REMARK 500 2 GLU P 121 -32.36 -37.93 REMARK 500 2 ARG P 128 74.61 -69.79 REMARK 500 2 DGL U 4 -133.84 -62.67 REMARK 500 3 SER P 3 61.44 67.92 REMARK 500 3 ALA P 8 -166.77 77.55 REMARK 500 3 ALA P 9 126.75 65.51 REMARK 500 3 TYR P 20 -178.34 60.57 REMARK 500 3 GLN P 27 -3.49 -140.60 REMARK 500 3 ARG P 28 -68.03 -107.54 REMARK 500 3 ASN P 30 27.66 -162.77 REMARK 500 3 ASP P 37 29.04 45.45 REMARK 500 3 TYR P 39 67.08 -119.57 REMARK 500 3 ASN P 79 -76.70 -67.83 REMARK 500 3 ILE P 80 -38.75 -33.10 REMARK 500 3 ARG P 128 79.64 -68.97 REMARK 500 4 ASP P 7 -62.65 -90.03 REMARK 500 4 ALA P 8 -176.46 -172.95 REMARK 500 4 ALA P 9 138.68 63.39 REMARK 500 4 ASN P 11 124.25 178.68 REMARK 500 4 GLN P 15 -164.51 -109.16 REMARK 500 4 ARG P 28 -50.17 -122.83 REMARK 500 4 ASN P 30 11.05 -176.08 REMARK 500 4 ASP P 37 29.76 43.59 REMARK 500 4 THR P 70 -173.33 -170.26 REMARK 500 4 ASN P 79 -75.44 -67.50 REMARK 500 REMARK 500 THIS ENTRY HAS 232 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HI0381 RELATED DB: TARGETDB DBREF 2AIZ P 1 134 UNP M4PH67 M4PH67_HAEIF 1 134 DBREF 2AIZ U 3 7 PDB 2AIZ 2AIZ 3 7 SEQRES 1 P 134 CYS SER SER SER ASN ASN ASP ALA ALA GLY ASN GLY ALA SEQRES 2 P 134 ALA GLN THR PHE GLY GLY TYR SER VAL ALA ASP LEU GLN SEQRES 3 P 134 GLN ARG TYR ASN THR VAL TYR PHE GLY PHE ASP LYS TYR SEQRES 4 P 134 ASP ILE THR GLY GLU TYR VAL GLN ILE LEU ASP ALA HIS SEQRES 5 P 134 ALA ALA TYR LEU ASN ALA THR PRO ALA ALA LYS VAL LEU SEQRES 6 P 134 VAL GLU GLY ASN THR ASP GLU ARG GLY THR PRO GLU TYR SEQRES 7 P 134 ASN ILE ALA LEU GLY GLN ARG ARG ALA ASP ALA VAL LYS SEQRES 8 P 134 GLY TYR LEU ALA GLY LYS GLY VAL ASP ALA GLY LYS LEU SEQRES 9 P 134 GLY THR VAL SER TYR GLY GLU GLU LYS PRO ALA VAL LEU SEQRES 10 P 134 GLY HIS ASP GLU ALA ALA TYR SER LYS ASN ARG ARG ALA SEQRES 11 P 134 VAL LEU ALA TYR SEQRES 1 U 5 ALA DGL 6CL DAL DAL MODRES 2AIZ DGL U 4 GLU D-GLUTAMIC ACID MODRES 2AIZ 6CL U 5 LYS 6-CARBOXYLYSINE MODRES 2AIZ DAL U 6 ALA D-ALANINE MODRES 2AIZ DAL U 7 ALA D-ALANINE HET DGL U 4 15 HET 6CL U 5 24 HET DAL U 6 10 HET DAL U 7 11 HET AMU U 101 36 HET UDP U 102 35 HETNAM DGL D-GLUTAMIC ACID HETNAM 6CL 6-CARBOXYLYSINE HETNAM DAL D-ALANINE HETNAM AMU N-ACETYL-BETA-MURAMIC ACID HETNAM UDP URIDINE-5'-DIPHOSPHATE HETSYN AMU N-ACETYL-MURAMIC ACID; BETA-N-ACETYLMURAMIC ACID FORMUL 2 DGL C5 H9 N O4 FORMUL 2 6CL C7 H15 N2 O4 1+ FORMUL 2 DAL 2(C3 H7 N O2) FORMUL 3 AMU C11 H19 N O8 FORMUL 4 UDP C9 H14 N2 O12 P2 HELIX 1 1 SER P 21 GLN P 26 1 6 HELIX 2 2 THR P 42 THR P 59 1 18 HELIX 3 3 THR P 75 LYS P 97 1 23 HELIX 4 4 ASP P 100 GLY P 102 5 3 HELIX 5 5 ASP P 120 ARG P 128 1 9 SHEET 1 A 4 THR P 31 TYR P 33 0 SHEET 2 A 4 ARG P 129 ALA P 133 -1 O ALA P 130 N VAL P 32 SHEET 3 A 4 VAL P 64 ASN P 69 -1 N LEU P 65 O ALA P 133 SHEET 4 A 4 LEU P 104 SER P 108 1 O GLY P 105 N VAL P 66 LINK C ALA U 3 N DGL U 4 1555 1555 1.33 LINK N ALA U 3 C10 AMU U 101 1555 1555 1.33 LINK C DGL U 4 N 6CL U 5 1555 1555 1.33 LINK C 6CL U 5 N DAL U 6 1555 1555 1.33 LINK C DAL U 6 N DAL U 7 1555 1555 1.32 LINK O1 AMU U 101 PB UDP U 102 1555 1555 1.60 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