HEADER OXIDOREDUCTASE 03-APR-08 3CQR TITLE CRYSTAL STRUCTURE OF THE LIPOCALIN DOMAIN OF VIOLAXANTHIN DE-EPOXIDASE TITLE 2 (VDE) AT PH5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIOLAXANTHIN DE-EPOXIDASE, CHLOROPLAST; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIPOCALIN DOMAIN (UNP RESIDUES 191-366); COMPND 5 SYNONYM: PROTEIN NON-PHOTOCHEMICAL QUENCHING 1, ATVXDE; COMPND 6 EC: 1.10.99.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: VDE1, AVDE1, NPQ1, VXDE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS LIPOCALIN, ENZYME, DE-EPOXIDASE, XANTHOPHYLL CYCLE, NON PHOTOCHEMICAL KEYWDS 2 QUENCHING, NPQ, VIOLAXANTHIN, ANTHERAXANTHIN, ZEAXANTHIN, KEYWDS 3 CHLOROPLAST, MEMBRANE, OXIDOREDUCTASE, THYLAKOID, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR P.ARNOUX,T.MOROSINOTTO,D.PIGNOL REVDAT 2 26-DEC-12 3CQR 1 JRNL VERSN REVDAT 1 21-APR-09 3CQR 0 JRNL AUTH P.ARNOUX,T.MOROSINOTTO,G.SAGA,R.BASSI,D.PIGNOL JRNL TITL A STRUCTURAL BASIS FOR THE PH-DEPENDENT XANTHOPHYLL CYCLE IN JRNL TITL 2 ARABIDOPSIS THALIANA. JRNL REF PLANT CELL V. 21 2036 2009 JRNL REFN ISSN 1040-4651 JRNL PMID 19638474 JRNL DOI 10.1105/TPC.109.068007 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 37869 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1996 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2645 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2773 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : 0.18000 REMARK 3 B12 (A**2) : 0.00000 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): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.965 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2889 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3941 ; 1.797 ; 1.924 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 8.609 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;37.544 ;24.304 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 433 ;16.884 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.871 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 402 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2323 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1151 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1928 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 180 ; 0.156 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.026 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 126 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.261 ; 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): 1758 ; 1.328 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2791 ; 2.215 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1317 ; 3.412 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1150 ; 5.152 ; 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-08. REMARK 100 THE RCSB ID CODE IS RCSB047099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39345 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : 0.26700 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE TRIHYDRATE PH5, REMARK 280 AMMONIUM SULFATE 2.0M, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 -1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 61.14850 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.16850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.58425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 61.14850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 118.75275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.75275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.14850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.58425 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 61.14850 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.16850 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 61.14850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 79.16850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 61.14850 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 118.75275 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 39.58425 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.14850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 39.58425 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 118.75275 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 61.14850 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 61.14850 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 79.16850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: BIOLOGICAL UNIT IS A MONOMER AT PH7 AND A DIMER AT PH5. REMARK 300 THERE IS ONE BIOLOGICAL UNIT IN THE ASYMMETRIC UNIT AT PH5 (CHAINS REMARK 300 A, B) 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 61.14850 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 -1.000000 118.75275 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -118.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 61.14850 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 118.75275 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 513 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 496 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 437 LIES ON A SPECIAL POSITION. 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 77 REMARK 465 ASP A 78 REMARK 465 LEU A 79 REMARK 465 GLY A 80 REMARK 465 GLU A 252 REMARK 465 PRO A 253 REMARK 465 ARG A 254 REMARK 465 SER A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 HIS A 258 REMARK 465 HIS A 259 REMARK 465 HIS A 260 REMARK 465 HIS A 261 REMARK 465 MET B 77 REMARK 465 ASP B 78 REMARK 465 LEU B 79 REMARK 465 GLY B 80 REMARK 465 GLU B 81 REMARK 465 GLU B 252 REMARK 465 PRO B 253 REMARK 465 ARG B 254 REMARK 465 SER B 255 REMARK 465 HIS B 256 REMARK 465 HIS B 257 REMARK 465 HIS B 258 REMARK 465 HIS B 259 REMARK 465 HIS B 260 REMARK 465 HIS B 261 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 CB GLU A 81 O HOH A 465 2.08 REMARK 500 OG SER B 136 NH2 ARG B 138 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 434 O HOH B 485 5555 2.15 REMARK 500 O HOH A 489 O HOH B 462 5555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP B 169 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES 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 ASP A 169 -11.33 40.35 REMARK 500 GLU A 171 -134.48 61.46 REMARK 500 TRP A 205 146.44 -174.40 REMARK 500 ASP B 169 -12.28 40.96 REMARK 500 GLU B 171 -113.07 51.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 168 ASP A 169 129.31 REMARK 500 HIS B 168 ASP B 169 130.25 REMARK 500 CYS B 249 GLY B 250 -119.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 110 21.2 L L OUTSIDE RANGE REMARK 500 ASN A 170 23.2 L L OUTSIDE RANGE 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 GD A 401 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 483 O REMARK 620 2 GLU A 81 N 115.5 REMARK 620 3 GLU A 81 O 87.3 61.5 REMARK 620 4 HOH A 474 O 130.4 90.2 141.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GD A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CQN RELATED DB: PDB REMARK 900 LIPOCALIN DOMAIN OF VDE AT PH7 DBREF 3CQR A 78 253 UNP Q39249 VDE_ARATH 191 366 DBREF 3CQR B 78 253 UNP Q39249 VDE_ARATH 191 366 SEQADV 3CQR MET A 77 UNP Q39249 INITIATING METHIONINE SEQADV 3CQR ARG A 254 UNP Q39249 EXPRESSION TAG SEQADV 3CQR SER A 255 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 256 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 257 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 258 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 259 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 260 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS A 261 UNP Q39249 EXPRESSION TAG SEQADV 3CQR MET B 77 UNP Q39249 INITIATING METHIONINE SEQADV 3CQR ARG B 254 UNP Q39249 EXPRESSION TAG SEQADV 3CQR SER B 255 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 256 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 257 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 258 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 259 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 260 UNP Q39249 EXPRESSION TAG SEQADV 3CQR HIS B 261 UNP Q39249 EXPRESSION TAG SEQRES 1 A 185 MET ASP LEU GLY GLU PHE PRO ALA PRO ASP PRO SER VAL SEQRES 2 A 185 LEU VAL GLN ASN PHE ASN ILE SER ASP PHE ASN GLY LYS SEQRES 3 A 185 TRP TYR ILE THR SER GLY LEU ASN PRO THR PHE ASP ALA SEQRES 4 A 185 PHE ASP CYS GLN LEU HIS GLU PHE HIS THR GLU GLY ASP SEQRES 5 A 185 ASN LYS LEU VAL GLY ASN ILE SER TRP ARG ILE LYS THR SEQRES 6 A 185 LEU ASP SER GLY PHE PHE THR ARG SER ALA VAL GLN LYS SEQRES 7 A 185 PHE VAL GLN ASP PRO ASN GLN PRO GLY VAL LEU TYR ASN SEQRES 8 A 185 HIS ASP ASN GLU TYR LEU HIS TYR GLN ASP ASP TRP TYR SEQRES 9 A 185 ILE LEU SER SER LYS ILE GLU ASN LYS PRO GLU ASP TYR SEQRES 10 A 185 ILE PHE VAL TYR TYR ARG GLY ARG ASN ASP ALA TRP ASP SEQRES 11 A 185 GLY TYR GLY GLY ALA VAL VAL TYR THR ARG SER SER VAL SEQRES 12 A 185 LEU PRO ASN SER ILE ILE PRO GLU LEU GLU LYS ALA ALA SEQRES 13 A 185 LYS SER ILE GLY ARG ASP PHE SER THR PHE ILE ARG THR SEQRES 14 A 185 ASP ASN THR CYS GLY PRO GLU PRO ARG SER HIS HIS HIS SEQRES 15 A 185 HIS HIS HIS SEQRES 1 B 185 MET ASP LEU GLY GLU PHE PRO ALA PRO ASP PRO SER VAL SEQRES 2 B 185 LEU VAL GLN ASN PHE ASN ILE SER ASP PHE ASN GLY LYS SEQRES 3 B 185 TRP TYR ILE THR SER GLY LEU ASN PRO THR PHE ASP ALA SEQRES 4 B 185 PHE ASP CYS GLN LEU HIS GLU PHE HIS THR GLU GLY ASP SEQRES 5 B 185 ASN LYS LEU VAL GLY ASN ILE SER TRP ARG ILE LYS THR SEQRES 6 B 185 LEU ASP SER GLY PHE PHE THR ARG SER ALA VAL GLN LYS SEQRES 7 B 185 PHE VAL GLN ASP PRO ASN GLN PRO GLY VAL LEU TYR ASN SEQRES 8 B 185 HIS ASP ASN GLU TYR LEU HIS TYR GLN ASP ASP TRP TYR SEQRES 9 B 185 ILE LEU SER SER LYS ILE GLU ASN LYS PRO GLU ASP TYR SEQRES 10 B 185 ILE PHE VAL TYR TYR ARG GLY ARG ASN ASP ALA TRP ASP SEQRES 11 B 185 GLY TYR GLY GLY ALA VAL VAL TYR THR ARG SER SER VAL SEQRES 12 B 185 LEU PRO ASN SER ILE ILE PRO GLU LEU GLU LYS ALA ALA SEQRES 13 B 185 LYS SER ILE GLY ARG ASP PHE SER THR PHE ILE ARG THR SEQRES 14 B 185 ASP ASN THR CYS GLY PRO GLU PRO ARG SER HIS HIS HIS SEQRES 15 B 185 HIS HIS HIS HET GD A 401 1 HET GD B 402 1 HET GD B 403 1 HETNAM GD GADOLINIUM ATOM FORMUL 3 GD 3(GD) FORMUL 6 HOH *178(H2 O) HELIX 1 1 ASP A 86 LEU A 90 5 5 HELIX 2 2 ASN A 95 ASN A 100 5 6 HELIX 3 3 ASN A 170 LEU A 173 5 4 HELIX 4 4 PRO A 221 SER A 223 5 3 HELIX 5 5 ILE A 224 ILE A 235 1 12 HELIX 6 6 ASP A 238 PHE A 242 5 5 HELIX 7 7 ASP B 86 LEU B 90 5 5 HELIX 8 8 ASN B 95 ASN B 100 5 6 HELIX 9 9 ASN B 170 LEU B 173 5 4 HELIX 10 10 PRO B 221 SER B 223 5 3 HELIX 11 11 ILE B 224 ILE B 235 1 12 HELIX 12 12 ASP B 238 PHE B 242 5 5 SHEET 1 A10 ILE A 243 ARG A 244 0 SHEET 2 A10 GLY A 101 GLY A 108 -1 N GLY A 108 O ILE A 243 SHEET 3 A10 TRP A 205 THR A 215 -1 O THR A 215 N TYR A 104 SHEET 4 A10 TYR A 193 ASN A 202 -1 N ILE A 194 O TYR A 214 SHEET 5 A10 TYR A 175 LYS A 185 -1 N ASP A 178 O ARG A 199 SHEET 6 A10 VAL A 164 ASN A 167 -1 N LEU A 165 O TRP A 179 SHEET 7 A10 PHE A 146 GLN A 157 -1 N VAL A 156 O TYR A 166 SHEET 8 A10 LYS A 130 LYS A 140 -1 N LEU A 131 O PHE A 155 SHEET 9 A10 LEU A 120 GLU A 126 -1 N HIS A 124 O VAL A 132 SHEET 10 A10 GLY A 101 GLY A 108 -1 N TRP A 103 O HIS A 121 SHEET 1 B10 ILE B 243 ARG B 244 0 SHEET 2 B10 GLY B 101 GLY B 108 -1 N GLY B 108 O ILE B 243 SHEET 3 B10 TYR B 208 THR B 215 -1 O THR B 215 N TYR B 104 SHEET 4 B10 TYR B 193 ASN B 202 -1 N ILE B 194 O TYR B 214 SHEET 5 B10 TYR B 175 LYS B 185 -1 N ASP B 178 O ARG B 199 SHEET 6 B10 VAL B 164 ASN B 167 -1 N LEU B 165 O TRP B 179 SHEET 7 B10 PHE B 146 GLN B 157 -1 N VAL B 156 O TYR B 166 SHEET 8 B10 LYS B 130 LYS B 140 -1 N ILE B 135 O ALA B 151 SHEET 9 B10 LEU B 120 GLU B 126 -1 N HIS B 124 O VAL B 132 SHEET 10 B10 GLY B 101 GLY B 108 -1 N TRP B 103 O HIS B 121 SSBOND 1 CYS A 118 CYS A 249 1555 1555 2.03 SSBOND 2 CYS B 118 CYS B 249 1555 1555 2.04 LINK GD GD A 401 O HOH A 483 1555 1555 2.33 LINK N GLU A 81 GD GD A 401 1555 1555 2.68 LINK O GLU A 81 GD GD A 401 1555 1555 3.08 LINK GD GD A 401 O HOH A 474 1555 1555 3.40 SITE 1 AC1 2 GLU A 81 PHE A 82 CRYST1 122.297 122.297 158.337 90.00 90.00 90.00 I 41 2 2 32 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 0.008177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006316 0.00000