HEADER SIGNALING PROTEIN 25-JAN-07 2OOL TITLE CRYSTAL STRUCTURE OF THE CHROMOPHORE-BINDING DOMAIN OF AN UNUSUAL TITLE 2 BACTERIOPHYTOCHROME RPBPHP3 FROM R. PALUSTRIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CHORMOPHORE BINDING DOMAIN (RESIDUES: 1-337); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 258594; SOURCE 4 STRAIN: CGA009; SOURCE 5 GENE: PHYB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSETB KEYWDS BACTERIOPHYTOCHROME, PHOTOCONVERSION, PHOTORECEPTOR, BILIVERDIN, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.YANG,E.A.STOJKOVIC,J.KUK,K.MOFFAT REVDAT 7 30-AUG-23 2OOL 1 COMPND REMARK HETNAM LINK REVDAT 6 18-OCT-17 2OOL 1 REMARK REVDAT 5 04-APR-12 2OOL 1 FORMUL HETATM HETNAM REVDAT 4 13-JUL-11 2OOL 1 VERSN REVDAT 3 24-FEB-09 2OOL 1 VERSN REVDAT 2 21-AUG-07 2OOL 1 JRNL REVDAT 1 10-JUL-07 2OOL 0 JRNL AUTH X.YANG,E.A.STOJKOVIC,J.KUK,K.MOFFAT JRNL TITL CRYSTAL STRUCTURE OF THE CHROMOPHORE BINDING DOMAIN OF AN JRNL TITL 2 UNUSUAL BACTERIOPHYTOCHROME, RPBPHP3, REVEALS RESIDUES THAT JRNL TITL 3 MODULATE PHOTOCONVERSION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 12571 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17640891 JRNL DOI 10.1073/PNAS.0701737104 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 43956 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 3595 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2880 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 217 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4731 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 215 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.38000 REMARK 3 B22 (A**2) : 2.38000 REMARK 3 B33 (A**2) : -3.56000 REMARK 3 B12 (A**2) : 1.19000 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): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.889 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4995 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3374 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6833 ; 1.579 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8110 ; 0.982 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 611 ; 6.508 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 227 ;34.836 ;22.467 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 773 ;16.567 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;18.399 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 765 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5575 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1029 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1011 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3485 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2401 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2577 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 202 ; 0.156 ; 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): 12 ; 0.461 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.425 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.154 ; 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): 3974 ; 1.075 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1198 ; 0.186 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4985 ; 1.235 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2216 ; 1.965 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1846 ; 2.671 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 333 REMARK 3 ORIGIN FOR THE GROUP (A): 83.2949 9.6527 17.2499 REMARK 3 T TENSOR REMARK 3 T11: -0.0297 T22: -0.4463 REMARK 3 T33: -0.2347 T12: -0.0165 REMARK 3 T13: -0.0265 T23: -0.0599 REMARK 3 L TENSOR REMARK 3 L11: 1.3917 L22: 2.6738 REMARK 3 L33: 2.2950 L12: -0.4807 REMARK 3 L13: -0.2725 L23: -0.4716 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: -0.0852 S13: 0.1463 REMARK 3 S21: 0.0416 S22: -0.0455 S23: 0.1419 REMARK 3 S31: -0.0232 S32: -0.0599 S33: 0.0275 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 27 B 330 REMARK 3 ORIGIN FOR THE GROUP (A): 52.4504 23.3541 33.1112 REMARK 3 T TENSOR REMARK 3 T11: -0.0348 T22: -0.0364 REMARK 3 T33: 0.0486 T12: 0.1037 REMARK 3 T13: 0.0323 T23: 0.0721 REMARK 3 L TENSOR REMARK 3 L11: 1.3233 L22: 2.2329 REMARK 3 L33: 2.7600 L12: -0.6445 REMARK 3 L13: -0.5926 L23: 1.1123 REMARK 3 S TENSOR REMARK 3 S11: -0.1254 S12: -0.0007 S13: -0.2306 REMARK 3 S21: -0.0032 S22: 0.1735 S23: 0.0522 REMARK 3 S31: 0.1502 S32: -0.3194 S33: -0.0481 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2OOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-06; 09-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 14-BM-C; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9; 0.97 REMARK 200 MONOCHROMATOR : SI(III) DOUBLE CRYSTAL; BEND REMARK 200 CYLINDRICAL GE(111) MONOCHROMATOR REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58049 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, RESOLVE 2.06 REMARK 200 STARTING MODEL: MODIFIED PDB ENTRY 1ZTU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION OF 12MG/ML IN REMARK 280 100 MM TRI-SODIUM CITRATE PH 5.6, 6% ISOPROPANOL (V/V), AND 7% REMARK 280 PEG 4000 (W/V), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY EXISTS AS A DIMER IN THE ASYMMETRIC REMARK 300 UNIT WITH THE 6-HELIX BUNDLE AT THE DIMER INTERFACE. 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: 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 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 A 442 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 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 PRO A 7 REMARK 465 GLY A 8 REMARK 465 GLN A 9 REMARK 465 PRO A 10 REMARK 465 MET A 11 REMARK 465 ALA A 12 REMARK 465 SER A 13 REMARK 465 ALA A 14 REMARK 465 THR A 15 REMARK 465 ASP A 16 REMARK 465 PRO A 17 REMARK 465 SER A 18 REMARK 465 GLY A 19 REMARK 465 ARG A 20 REMARK 465 LEU A 21 REMARK 465 ALA A 22 REMARK 465 LEU A 23 REMARK 465 ASP A 24 REMARK 465 LEU A 25 REMARK 465 GLY A 97 REMARK 465 ASP A 98 REMARK 465 PRO A 99 REMARK 465 ALA A 100 REMARK 465 VAL A 334 REMARK 465 ARG A 335 REMARK 465 HIS A 336 REMARK 465 SER A 337 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 SER B 5 REMARK 465 ASP B 6 REMARK 465 PRO B 7 REMARK 465 GLY B 8 REMARK 465 GLN B 9 REMARK 465 PRO B 10 REMARK 465 MET B 11 REMARK 465 ALA B 12 REMARK 465 SER B 13 REMARK 465 ALA B 14 REMARK 465 THR B 15 REMARK 465 ASP B 16 REMARK 465 PRO B 17 REMARK 465 SER B 18 REMARK 465 GLY B 19 REMARK 465 ARG B 20 REMARK 465 LEU B 21 REMARK 465 ALA B 22 REMARK 465 LEU B 23 REMARK 465 ASP B 24 REMARK 465 LEU B 25 REMARK 465 THR B 26 REMARK 465 GLY B 97 REMARK 465 ASP B 98 REMARK 465 PRO B 99 REMARK 465 ALA B 100 REMARK 465 SER B 139 REMARK 465 ARG B 140 REMARK 465 TYR B 141 REMARK 465 THR B 142 REMARK 465 ILE B 333 REMARK 465 VAL B 334 REMARK 465 ARG B 335 REMARK 465 HIS B 336 REMARK 465 SER B 337 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 68 CG CD OE1 NE2 REMARK 480 GLU A 144 CG CD OE1 OE2 REMARK 480 VAL A 274 N CA C O CB CG1 CG2 REMARK 480 HIS B 80 CG ND1 CD2 CE1 NE2 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 NH2 ARG A 106 NH2 ARG A 106 5556 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 144 CB GLU A 144 CG 0.121 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 106 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -4.2 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 GLU A 27 6.23 -67.26 REMARK 500 THR A 51 -89.09 -73.40 REMARK 500 LEU A 94 -70.77 -74.63 REMARK 500 HIS A 95 40.15 -70.25 REMARK 500 TYR A 141 44.81 -140.43 REMARK 500 ASP A 209 -2.39 67.80 REMARK 500 THR B 51 -81.16 -77.51 REMARK 500 ASN B 75 -1.23 73.91 REMARK 500 LEU B 94 25.92 -78.77 REMARK 500 HIS B 95 -84.31 -104.10 REMARK 500 ASP B 209 -2.14 75.62 REMARK 500 ARG B 304 107.04 -164.05 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 ASN B 143 GLU B 144 148.63 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 LBV A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LBV B 400 DBREF 2OOL A 1 337 UNP Q6N5G2 Q6N5G2_RHOPA 1 337 DBREF 2OOL B 1 337 UNP Q6N5G2 Q6N5G2_RHOPA 1 337 SEQRES 1 A 337 MET SER SER ARG SER ASP PRO GLY GLN PRO MET ALA SER SEQRES 2 A 337 ALA THR ASP PRO SER GLY ARG LEU ALA LEU ASP LEU THR SEQRES 3 A 337 GLU CYS ASP ARG GLU PRO ILE HIS ILE PRO GLY ALA ILE SEQRES 4 A 337 GLN PRO HIS GLY TYR LEU PHE VAL VAL SER GLU THR ASP SEQRES 5 A 337 LEU ARG ILE ALA SER VAL SER ALA ASN VAL GLU ASP LEU SEQRES 6 A 337 LEU ARG GLN PRO PRO ALA SER LEU LEU ASN VAL PRO ILE SEQRES 7 A 337 ALA HIS TYR LEU THR ALA ALA SER ALA ALA ARG LEU THR SEQRES 8 A 337 HIS ALA LEU HIS GLY GLY ASP PRO ALA ALA ILE ASN PRO SEQRES 9 A 337 ILE ARG LEU ASP VAL VAL THR PRO ASP GLY GLU ARG ALA SEQRES 10 A 337 PHE ASN GLY ILE LEU HIS ARG HIS ASP SER ILE VAL ILE SEQRES 11 A 337 LEU GLU LEU GLU PRO ARG ASP GLU SER ARG TYR THR ASN SEQRES 12 A 337 GLU PHE PHE ARG SER VAL ARG VAL ALA ILE ARG ARG LEU SEQRES 13 A 337 GLN THR ALA ALA ASP LEU PRO THR ALA CYS TRP ILE ALA SEQRES 14 A 337 ALA SER GLU VAL ARG ARG ILE THR GLY PHE ASP ARG ILE SEQRES 15 A 337 LYS VAL TYR GLN PHE ALA ALA ASP TRP SER GLY GLN VAL SEQRES 16 A 337 ILE ALA GLU ASP ARG ASP SER GLY ILE PRO SER LEU LEU SEQRES 17 A 337 ASP PHE HIS PHE PRO SER SER ASP ILE PRO ALA GLN SER SEQRES 18 A 337 ARG ALA LEU TYR THR ILE ASN PRO VAL ARG ILE ILE PRO SEQRES 19 A 337 ASP ILE GLY TYR ARG PRO SER PRO LEU VAL PRO ASP ILE SEQRES 20 A 337 ASN PRO ARG LEU GLY GLY PRO ILE ASP LEU SER PHE SER SEQRES 21 A 337 VAL LEU ARG SER VAL SER PRO THR HIS LEU GLU TYR MET SEQRES 22 A 337 VAL ASN MET GLY MET HIS ALA ALA MET SER ILE SER ILE SEQRES 23 A 337 VAL ARG ASP ASN ARG LEU TRP GLY MET ILE SER CYS HIS SEQRES 24 A 337 ASN LEU THR PRO ARG PHE VAL SER TYR GLU VAL ARG GLN SEQRES 25 A 337 ALA CYS GLU LEU ILE ALA GLN VAL LEU THR TRP GLN ILE SEQRES 26 A 337 GLY VAL LEU GLU GLU ALA GLU ILE VAL ARG HIS SER SEQRES 1 B 337 MET SER SER ARG SER ASP PRO GLY GLN PRO MET ALA SER SEQRES 2 B 337 ALA THR ASP PRO SER GLY ARG LEU ALA LEU ASP LEU THR SEQRES 3 B 337 GLU CYS ASP ARG GLU PRO ILE HIS ILE PRO GLY ALA ILE SEQRES 4 B 337 GLN PRO HIS GLY TYR LEU PHE VAL VAL SER GLU THR ASP SEQRES 5 B 337 LEU ARG ILE ALA SER VAL SER ALA ASN VAL GLU ASP LEU SEQRES 6 B 337 LEU ARG GLN PRO PRO ALA SER LEU LEU ASN VAL PRO ILE SEQRES 7 B 337 ALA HIS TYR LEU THR ALA ALA SER ALA ALA ARG LEU THR SEQRES 8 B 337 HIS ALA LEU HIS GLY GLY ASP PRO ALA ALA ILE ASN PRO SEQRES 9 B 337 ILE ARG LEU ASP VAL VAL THR PRO ASP GLY GLU ARG ALA SEQRES 10 B 337 PHE ASN GLY ILE LEU HIS ARG HIS ASP SER ILE VAL ILE SEQRES 11 B 337 LEU GLU LEU GLU PRO ARG ASP GLU SER ARG TYR THR ASN SEQRES 12 B 337 GLU PHE PHE ARG SER VAL ARG VAL ALA ILE ARG ARG LEU SEQRES 13 B 337 GLN THR ALA ALA ASP LEU PRO THR ALA CYS TRP ILE ALA SEQRES 14 B 337 ALA SER GLU VAL ARG ARG ILE THR GLY PHE ASP ARG ILE SEQRES 15 B 337 LYS VAL TYR GLN PHE ALA ALA ASP TRP SER GLY GLN VAL SEQRES 16 B 337 ILE ALA GLU ASP ARG ASP SER GLY ILE PRO SER LEU LEU SEQRES 17 B 337 ASP PHE HIS PHE PRO SER SER ASP ILE PRO ALA GLN SER SEQRES 18 B 337 ARG ALA LEU TYR THR ILE ASN PRO VAL ARG ILE ILE PRO SEQRES 19 B 337 ASP ILE GLY TYR ARG PRO SER PRO LEU VAL PRO ASP ILE SEQRES 20 B 337 ASN PRO ARG LEU GLY GLY PRO ILE ASP LEU SER PHE SER SEQRES 21 B 337 VAL LEU ARG SER VAL SER PRO THR HIS LEU GLU TYR MET SEQRES 22 B 337 VAL ASN MET GLY MET HIS ALA ALA MET SER ILE SER ILE SEQRES 23 B 337 VAL ARG ASP ASN ARG LEU TRP GLY MET ILE SER CYS HIS SEQRES 24 B 337 ASN LEU THR PRO ARG PHE VAL SER TYR GLU VAL ARG GLN SEQRES 25 B 337 ALA CYS GLU LEU ILE ALA GLN VAL LEU THR TRP GLN ILE SEQRES 26 B 337 GLY VAL LEU GLU GLU ALA GLU ILE VAL ARG HIS SER HET LBV A 400 44 HET LBV B 400 43 HETNAM LBV 3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3- HETNAM 2 LBV METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4- HETNAM 3 LBV METHYL-PYRROL-1-IUM -2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3- HETNAM 4 LBV ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2- HETNAM 5 LBV YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3- YL]PROPANOIC HETNAM 6 LBV ACID HETSYN LBV 2(R),3(E)- PHYTOCHROMOBILIN FORMUL 3 LBV 2(C33 H37 N4 O6 1+) FORMUL 5 HOH *215(H2 O) HELIX 1 1 GLU A 27 GLU A 31 5 5 HELIX 2 2 ASN A 61 ARG A 67 1 7 HELIX 3 3 PRO A 69 LEU A 74 5 6 HELIX 4 4 PRO A 77 LEU A 82 5 6 HELIX 5 5 THR A 83 HIS A 95 1 13 HELIX 6 6 TYR A 141 THR A 158 1 18 HELIX 7 7 ASP A 161 GLY A 178 1 18 HELIX 8 8 PRO A 213 ILE A 217 5 5 HELIX 9 9 PRO A 218 ASN A 228 1 11 HELIX 10 10 SER A 266 GLY A 277 1 12 HELIX 11 11 SER A 307 ILE A 333 1 27 HELIX 12 12 GLU B 27 GLU B 31 5 5 HELIX 13 13 ASN B 61 ARG B 67 1 7 HELIX 14 14 PRO B 69 LEU B 74 1 6 HELIX 15 15 PRO B 77 LEU B 82 5 6 HELIX 16 16 THR B 83 LEU B 94 1 12 HELIX 17 17 ASN B 143 GLN B 157 1 15 HELIX 18 18 ASP B 161 GLY B 178 1 18 HELIX 19 19 PRO B 218 ASN B 228 1 11 HELIX 20 20 SER B 266 GLY B 277 1 12 HELIX 21 21 SER B 307 GLU B 330 1 24 SHEET 1 A 7 ALA A 38 ILE A 39 0 SHEET 2 A 7 SER A 241 VAL A 244 -1 O SER A 241 N ILE A 39 SHEET 3 A 7 ILE A 55 SER A 59 -1 N VAL A 58 O VAL A 244 SHEET 4 A 7 TYR A 44 VAL A 48 -1 N VAL A 47 O ALA A 56 SHEET 5 A 7 ILE A 128 GLU A 134 -1 O LEU A 131 N PHE A 46 SHEET 6 A 7 GLY A 114 HIS A 125 -1 N ILE A 121 O GLU A 132 SHEET 7 A 7 ILE A 105 THR A 111 -1 N ILE A 105 O GLY A 120 SHEET 1 B 6 HIS A 211 PHE A 212 0 SHEET 2 B 6 GLY A 193 ARG A 200 -1 N GLY A 193 O PHE A 212 SHEET 3 B 6 ARG A 181 PHE A 187 -1 N ILE A 182 O ASP A 199 SHEET 4 B 6 ARG A 291 ASN A 300 -1 O MET A 295 N TYR A 185 SHEET 5 B 6 ALA A 280 ARG A 288 -1 N MET A 282 O CYS A 298 SHEET 6 B 6 VAL A 230 ILE A 233 -1 N ILE A 233 O ALA A 281 SHEET 1 C 7 ALA B 38 ILE B 39 0 SHEET 2 C 7 SER B 241 VAL B 244 -1 O SER B 241 N ILE B 39 SHEET 3 C 7 ILE B 55 SER B 59 -1 N VAL B 58 O VAL B 244 SHEET 4 C 7 TYR B 44 SER B 49 -1 N VAL B 47 O SER B 57 SHEET 5 C 7 ILE B 128 GLU B 134 -1 O LEU B 131 N PHE B 46 SHEET 6 C 7 GLY B 114 HIS B 125 -1 N ILE B 121 O GLU B 132 SHEET 7 C 7 ILE B 105 THR B 111 -1 N ILE B 105 O GLY B 120 SHEET 1 D 6 HIS B 211 PHE B 212 0 SHEET 2 D 6 GLY B 193 ARG B 200 -1 N GLY B 193 O PHE B 212 SHEET 3 D 6 ARG B 181 PHE B 187 -1 N ILE B 182 O ASP B 199 SHEET 4 D 6 ARG B 291 ASN B 300 -1 O HIS B 299 N ARG B 181 SHEET 5 D 6 ALA B 280 ARG B 288 -1 N ILE B 286 O TRP B 293 SHEET 6 D 6 VAL B 230 ILE B 233 -1 N ILE B 233 O ALA B 281 LINK SG CYS A 28 CBA LBV A 400 1555 1555 1.69 LINK SG CYS B 28 CBA LBV B 400 1555 1555 1.64 CISPEP 1 ASN A 103 PRO A 104 0 -6.46 CISPEP 2 VAL A 244 PRO A 245 0 -12.02 CISPEP 3 ASN B 103 PRO B 104 0 -3.12 CISPEP 4 VAL B 244 PRO B 245 0 -11.19 SITE 1 AC1 22 CYS A 28 LYS A 183 SER A 215 ASP A 216 SITE 2 AC1 22 ILE A 217 PRO A 218 SER A 221 TYR A 225 SITE 3 AC1 22 ARG A 263 VAL A 265 SER A 266 THR A 268 SITE 4 AC1 22 HIS A 269 TYR A 272 ALA A 281 SER A 283 SITE 5 AC1 22 SER A 297 HIS A 299 HOH A 410 HOH A 437 SITE 6 AC1 22 HOH A 439 HOH A 551 SITE 1 AC2 21 CYS B 28 LYS B 183 TYR B 185 VAL B 195 SITE 2 AC2 21 SER B 215 ASP B 216 ILE B 217 PRO B 218 SITE 3 AC2 21 SER B 221 TYR B 225 ARG B 263 VAL B 265 SITE 4 AC2 21 SER B 266 HIS B 269 TYR B 272 ALA B 281 SITE 5 AC2 21 SER B 283 SER B 297 HIS B 299 HOH B 432 SITE 6 AC2 21 HOH B 453 CRYST1 151.866 151.866 75.996 90.00 90.00 120.00 P 3 2 1 12 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 0.006585 0.003802 0.000000 0.00000 SCALE2 0.000000 0.007603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013159 0.00000