10 20 30 40 50 60 70 80 2QJ5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 06-JUL-07 2QJ5
TITLE PYP ULTRA-HIGH RESOLUTION OF A BACTERIAL PHOTORECEPTOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYP; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALORHODOSPIRA HALOPHILA; SOURCE 3 GENE: PYP; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI
KEYWDS PAS DOMAIN, SIGNALING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.D.COUREUX,Z.P.FAN,V.STOJANOFF,U.K.GENICK
REVDAT 3 24-FEB-09 2QJ5 1 VERSN REVDAT 2 08-JUL-08 2QJ5 1 JRNL REVDAT 1 20-MAY-08 2QJ5 0
JRNL AUTH P.D.COUREUX,Z.P.FAN,V.STOJANOFF,U.K.GENICK JRNL TITL PICOMETER-SCALE CONFORMATIONAL HETEROGENEITY JRNL TITL 2 SEPARATES FUNCTIONAL FROM NONFUNCTIONAL STATES OF JRNL TITL 3 A PHOTORECEPTOR PROTEIN. JRNL REF STRUCTURE V. 16 863 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18547519 JRNL DOI 10.1016/J.STR.2008.02.022
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 30823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1652 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1495 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.03000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.549 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1035 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1398 ; 1.359 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 130 ; 6.467 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;36.938 ;25.625 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 173 ;12.425 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 1.178 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 148 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 802 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 450 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 700 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 54 ; 0.071 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.177 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.146 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 659 ; 1.321 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1025 ; 1.979 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 449 ; 2.755 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 373 ; 3.653 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2QJ5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB043663.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.85 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : SI(111) CHANNEL CUT REMARK 200 MONOCHROMATOR TOROIDAL REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32475 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : 0.18000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1NWZ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 39% PEG 3000, 50 MM TRIS-HCL PH 9, REMARK 280 5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.38400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.19200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.78800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.59600 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.98000 REMARK 290 REMARK 290 REMARK: NULL
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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 114 REMARK 465 GLY A 115
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 106 CD CE NZ REMARK 470 ASP A 116 CG OD1 OD2
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 PHE A 75 -77.96 -130.07 REMARK 500 ASN A 89 91.85 -171.71 REMARK 500 ASP A 97 18.40 -143.66 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HC4 A 126
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QJ7 RELATED DB: PDB REMARK 900 PHOTOACTIVE YELLOW PROTEIN, LIGHT STATE
DBREF 2QJ5 A 1 125 UNP P16113 PYP_HALHA 1 125
SEQRES 1 A 125 MET GLU HIS VAL ALA PHE GLY SER GLU ASP ILE GLU ASN SEQRES 2 A 125 THR LEU ALA LYS MET ASP ASP GLY GLN LEU ASP GLY LEU SEQRES 3 A 125 ALA PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE SEQRES 4 A 125 LEU GLN TYR ASN ALA ALA GLU GLY ASP ILE THR GLY ARG SEQRES 5 A 125 ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS ASP SEQRES 6 A 125 VAL ALA PRO CYS THR ASP SER PRO GLU PHE TYR GLY LYS SEQRES 7 A 125 PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR MET SEQRES 8 A 125 PHE GLU TYR THR PHE ASP TYR GLN MET THR PRO THR LYS SEQRES 9 A 125 VAL LYS VAL HIS MET LYS LYS ALA LEU SER GLY ASP SER SEQRES 10 A 125 TYR TRP VAL PHE VAL LYS ARG VAL
HET HC4 A 126 11
HETNAM HC4 4'-HYDROXYCINNAMIC ACID
HETSYN HC4 PARA-COUMARIC ACID
FORMUL 2 HC4 C9 H8 O3 FORMUL 3 HOH *49(H2 O)
HELIX 1 1 ASP A 10 LYS A 17 1 8 HELIX 2 2 ASP A 19 GLY A 25 1 7 HELIX 3 3 ASN A 43 GLY A 51 1 9 HELIX 4 4 ASP A 53 ILE A 58 1 6 HELIX 5 5 ALA A 67 ASP A 71 5 5 HELIX 6 6 PHE A 75 GLY A 86 1 12
SHEET 1 A 5 ILE A 39 TYR A 42 0 SHEET 2 A 5 GLY A 29 LEU A 33 -1 N GLN A 32 O LEU A 40 SHEET 3 A 5 TYR A 118 ARG A 124 -1 O TYR A 118 N LEU A 33 SHEET 4 A 5 THR A 103 LYS A 111 -1 N LYS A 110 O TRP A 119 SHEET 5 A 5 ASN A 89 PHE A 96 -1 N PHE A 92 O VAL A 107
LINK SG CYS A 69 C1 HC4 A 126 1555 1555 1.81
SITE 1 AC1 9 ILE A 31 TYR A 42 GLU A 46 THR A 50 SITE 2 AC1 9 ALA A 67 PRO A 68 CYS A 69 PHE A 96 SITE 3 AC1 9 TYR A 98
CRYST1 40.779 40.779 117.576 90.00 90.00 120.00 P 65 6
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 0.024522 0.014158 0.000000 0.00000
SCALE2 0.000000 0.028316 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008505 0.00000