PDB Short entry for 1YBJ HEADER METAL BINDING PROTEIN 21-DEC-04 1YBJ TITLE STRUCTURAL AND DYNAMICS STUDIES OF BOTH APO AND HOLO FORMS OF THE TITLE 2 HEMOPHORE HASA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOPHORE HASA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEME ACQUISITION SYSTEM PROTEIN A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SERRATIA MARCESCENS; SOURCE 3 ORGANISM_TAXID: 615; SOURCE 4 GENE: HASA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: POP3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PAM238; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSYC150 KEYWDS ALPHA+BETA STRUCTURE, CURVED ANTI-PARALLEL BETA-SHEET, METAL BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.WOLFF,N.IZADI-PRUNEYRE,J.COUPRIE,M.HABECK,J.LINGE,W.RIEPING, AUTHOR 2 C.WANDERSMAN,M.NILGES,M.DELEPIERRE,A.LECROISEY REVDAT 4 02-MAR-22 1YBJ 1 REMARK REVDAT 3 12-MAY-09 1YBJ 1 JRNL REVDAT 2 24-FEB-09 1YBJ 1 VERSN REVDAT 1 27-DEC-05 1YBJ 0 JRNL AUTH N.WOLFF,N.IZADI-PRUNEYRE,J.COUPRIE,M.HABECK,J.LINGE, JRNL AUTH 2 W.RIEPING,C.WANDERSMAN,M.NILGES,M.DELEPIERRE,A.LECROISEY JRNL TITL COMPARATIVE ANALYSIS OF STRUCTURAL AND DYNAMIC PROPERTIES OF JRNL TITL 2 THE LOADED AND UNLOADED HEMOPHORE HASA: FUNCTIONAL JRNL TITL 3 IMPLICATIONS. JRNL REF J.MOL.BIOL. V. 376 517 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18164722 JRNL DOI 10.1016/J.JMB.2007.11.072 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, ARIA/CNS 2.0ALPHA REMARK 3 AUTHORS : LINGE, J., NILGES, M., HABECK, M., RIEPING, W. REMARK 3 (ARIA/CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 3537 REMARK 3 DISTANCE RESTRAINTS (WHERE 3145 WERE UNAMBIGUOUS AND 392 REMARK 3 AMBIGUOUS),111 PHI TORSION ANGLES AND 34 HYDROGEN BONDS. REMARK 4 REMARK 4 1YBJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031345. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 20MM SODIUM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8MM HASA 15N; 1.9MM HASA REMARK 210 15N,13C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA; 3D_15N-SEPARATED_NOESY; REMARK 210 3D_13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY 1.3.13, ARIA/CNS REMARK 210 2.0ALPHA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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 : 10 REMARK 210 REMARK 210 REMARK: H-BOND CONSTRAINTS ACCORDING TO THE AMIDE PROTON-DEUTERIUM REMARK 210 EXCHANGE MEASUREMENTS (15N HSQC EXPERIMENTS) 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 HE1 TYR A 74 HB3 LEU A 76 1.22 REMARK 500 HG13 ILE A 56 HG2 MET A 139 1.34 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 ASN A 5 49.40 -101.75 REMARK 500 1 SER A 8 80.48 -39.25 REMARK 500 1 SER A 9 -29.17 -173.70 REMARK 500 1 THR A 37 -73.55 -100.18 REMARK 500 1 ALA A 39 73.52 62.48 REMARK 500 1 PHE A 44 -178.44 60.60 REMARK 500 1 TYR A 45 -69.21 -142.02 REMARK 500 1 LEU A 49 -40.93 -154.67 REMARK 500 1 GLN A 62 42.35 33.77 REMARK 500 1 VAL A 63 -53.98 -121.83 REMARK 500 1 THR A 75 47.61 -81.87 REMARK 500 1 ALA A 81 115.43 72.36 REMARK 500 1 TYR A 85 -159.53 -153.95 REMARK 500 1 ASP A 89 -45.00 -132.14 REMARK 500 1 SER A 92 103.78 -167.22 REMARK 500 1 ASP A 101 -70.15 -144.81 REMARK 500 1 ASP A 111 -150.30 -104.48 REMARK 500 1 LEU A 159 -161.97 -104.40 REMARK 500 1 VAL A 174 -31.16 -170.51 REMARK 500 2 ASN A 5 49.97 -103.90 REMARK 500 2 SER A 8 77.15 -34.94 REMARK 500 2 SER A 9 -30.01 -173.35 REMARK 500 2 VAL A 29 0.38 -63.60 REMARK 500 2 THR A 37 -62.83 -107.92 REMARK 500 2 ASP A 38 -72.70 -75.91 REMARK 500 2 ALA A 39 87.04 68.97 REMARK 500 2 LEU A 49 40.76 -166.43 REMARK 500 2 GLN A 53 105.72 80.21 REMARK 500 2 GLN A 62 45.39 33.80 REMARK 500 2 LEU A 76 -92.77 42.09 REMARK 500 2 ALA A 81 128.37 72.63 REMARK 500 2 HIS A 82 60.28 38.09 REMARK 500 2 SER A 92 106.93 -162.82 REMARK 500 2 ASP A 101 -102.03 -87.89 REMARK 500 2 PRO A 110 93.90 -63.87 REMARK 500 2 ASP A 111 -155.56 -93.45 REMARK 500 2 LEU A 159 -167.93 -101.40 REMARK 500 2 SER A 163 -116.95 -87.17 REMARK 500 2 VAL A 174 -30.32 -167.87 REMARK 500 3 ASN A 5 46.82 -106.32 REMARK 500 3 SER A 8 73.56 -25.15 REMARK 500 3 SER A 9 -32.07 -174.64 REMARK 500 3 VAL A 29 2.64 -68.00 REMARK 500 3 ASN A 33 120.49 -173.22 REMARK 500 3 THR A 37 -67.07 -103.78 REMARK 500 3 ASP A 38 -75.35 -47.57 REMARK 500 3 ALA A 39 63.30 65.11 REMARK 500 3 PHE A 44 130.66 66.33 REMARK 500 3 LEU A 49 21.51 -164.44 REMARK 500 3 SER A 52 -144.75 -148.77 REMARK 500 REMARK 500 THIS ENTRY HAS 233 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1YBJ A 1 178 UNP Q54450 HASA_SERMA 2 179 SEQRES 1 A 178 ALA PHE SER VAL ASN TYR ASP SER SER PHE GLY GLY TYR SEQRES 2 A 178 SER ILE HIS ASP TYR LEU GLY GLN TRP ALA SER THR PHE SEQRES 3 A 178 GLY ASP VAL ASN HIS THR ASN GLY ASN VAL THR ASP ALA SEQRES 4 A 178 ASN SER GLY GLY PHE TYR GLY GLY SER LEU SER GLY SER SEQRES 5 A 178 GLN TYR ALA ILE SER SER THR ALA ASN GLN VAL THR ALA SEQRES 6 A 178 PHE VAL ALA GLY GLY ASN LEU THR TYR THR LEU PHE ASN SEQRES 7 A 178 GLU PRO ALA HIS THR LEU TYR GLY GLN LEU ASP SER LEU SEQRES 8 A 178 SER PHE GLY ASP GLY LEU SER GLY GLY ASP THR SER PRO SEQRES 9 A 178 TYR SER ILE GLN VAL PRO ASP VAL SER PHE GLY GLY LEU SEQRES 10 A 178 ASN LEU SER SER LEU GLN ALA GLN GLY HIS ASP GLY VAL SEQRES 11 A 178 VAL HIS GLN VAL VAL TYR GLY LEU MET SER GLY ASP THR SEQRES 12 A 178 GLY ALA LEU GLU THR ALA LEU ASN GLY ILE LEU ASP ASP SEQRES 13 A 178 TYR GLY LEU SER VAL ASN SER THR PHE ASP GLN VAL ALA SEQRES 14 A 178 ALA ALA THR ALA VAL GLY VAL GLN HIS HELIX 1 1 SER A 14 ASP A 28 1 15 HELIX 2 2 GLY A 129 SER A 140 1 12 HELIX 3 3 ALA A 145 GLY A 158 1 14 HELIX 4 4 THR A 164 VAL A 174 1 11 SHEET 1 A 5 SER A 3 VAL A 4 0 SHEET 2 A 5 SER A 106 GLY A 115 -1 O GLY A 115 N SER A 3 SHEET 3 A 5 SER A 92 SER A 98 -1 N GLY A 96 O GLN A 108 SHEET 4 A 5 THR A 64 TYR A 74 -1 N VAL A 67 O SER A 92 SHEET 5 A 5 GLN A 53 SER A 57 -1 N ILE A 56 O PHE A 66 SHEET 1 B 6 SER A 3 VAL A 4 0 SHEET 2 B 6 SER A 106 GLY A 115 -1 O GLY A 115 N SER A 3 SHEET 3 B 6 SER A 92 SER A 98 -1 N GLY A 96 O GLN A 108 SHEET 4 B 6 THR A 64 TYR A 74 -1 N VAL A 67 O SER A 92 SHEET 5 B 6 LEU A 84 SER A 90 -1 O ASP A 89 N GLY A 69 SHEET 6 B 6 LEU A 119 SER A 121 -1 O LEU A 119 N LEU A 88 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