HEADER PHOTOSYNTHESIS 07-SEP-17 5OY5 TITLE MONOMERIC CRYSTAL STRUCTURE OF RPBPHP1 PHOTOSENSORY CORE DOMAIN FROM TITLE 2 THE BACTERIUM RHODOPSEUDOMONAS PALUSTRIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BPHP1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS (STRAIN ATCC BAA-98 SOURCE 3 / CGA009); SOURCE 4 ORGANISM_TAXID: 258594; SOURCE 5 STRAIN: ATCC BAA-98 / CGA009; SOURCE 6 ATCC: BAA-98; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BACTERIOPHYTOCHROME, GENE REPRESSOR, PHOTOSYNTHESIS, BILIVERDIN EXPDTA X-RAY DIFFRACTION AUTHOR M.Z.PAPIZ,D.BELLINI REVDAT 2 17-JAN-24 5OY5 1 REMARK REVDAT 1 06-FEB-19 5OY5 0 JRNL AUTH M.Z.PAPIZ,D.BELLINI JRNL TITL INSIGHTS INTO THE LIGHT-INDUCED MOLECULAR SWITCH OF THE JRNL TITL 2 BACTERIOPHYTOCHROME RPBPHP1 PROBED BY SAXS, MODELLING AND JRNL TITL 3 UV-VIS OPTICAL PROPERTIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.BELLINI,M.Z.PAPIZ REMARK 1 TITL STRUCTURE OF A BACTERIOPHYTOCHROME AND LIGHT-STIMULATED REMARK 1 TITL 2 PROTOMER SWAPPING WITH A GENE REPRESSOR. REMARK 1 REF STRUCTURE V. 20 1436 2012 REMARK 1 REFN ISSN 1878-4186 REMARK 1 PMID 22795083 REMARK 1 DOI 10.1016/J.STR.2012.06.002 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 34645 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1840 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2490 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.93000 REMARK 3 B12 (A**2) : -0.14000 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): 0.238 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.214 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3929 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5348 ; 2.011 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 7.654 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;35.642 ;22.784 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 619 ;22.127 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.153 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 595 ; 0.149 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3024 ; 0.020 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1963 ; 3.703 ; 3.120 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2452 ; 5.939 ; 4.672 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1964 ; 4.785 ; 3.398 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6147 ;18.032 ;44.504 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 8 A 340 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1660 -2.9210 18.0260 REMARK 3 T TENSOR REMARK 3 T11: 0.5413 T22: 0.1294 REMARK 3 T33: 0.0271 T12: -0.0587 REMARK 3 T13: -0.0070 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 1.6810 L22: 2.6793 REMARK 3 L33: 3.4007 L12: 0.8053 REMARK 3 L13: 0.1909 L23: 0.1655 REMARK 3 S TENSOR REMARK 3 S11: 0.0393 S12: -0.3023 S13: -0.1080 REMARK 3 S21: 0.3593 S22: -0.1673 S23: -0.1323 REMARK 3 S31: 0.0040 S32: -0.0688 S33: 0.1280 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 : A 341 A 507 REMARK 3 ORIGIN FOR THE GROUP (A): 28.6340 22.5540 39.5550 REMARK 3 T TENSOR REMARK 3 T11: 0.9417 T22: 0.4562 REMARK 3 T33: 0.2182 T12: -0.5785 REMARK 3 T13: 0.1384 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 3.3774 L22: 2.2847 REMARK 3 L33: 6.8019 L12: 0.9555 REMARK 3 L13: 2.7447 L23: 2.1974 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: -0.2605 S13: -0.1932 REMARK 3 S21: -0.2486 S22: 0.1985 S23: -0.3546 REMARK 3 S31: -1.2254 S32: 0.8913 S33: -0.1996 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5OY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006541. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : KIRKPATRICK BAEZ (KB) BIMORPH REMARK 200 MIRROR PAIR FOR HORIZONTAL AND REMARK 200 VERTICAL FOCUSSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34645 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 79.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : 0.62000 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4GW9 REMARK 200 REMARK 200 REMARK: BIPYRAMID 0.6 MM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% PGA (POLY-GAMMA-GLUTAMIC ACID REMARK 280 POLYMER), 200 MM KBR AND 100 MM TRISHCL PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 299.44667 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 149.72333 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 224.58500 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 74.86167 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 374.30833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 299.44667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 149.72333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 74.86167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 224.58500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 374.30833 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ALA A 3 REMARK 465 GLY A 4 REMARK 465 HIS A 5 REMARK 465 ALA A 6 REMARK 465 SER A 7 REMARK 465 ASP A 451 REMARK 465 PRO A 452 REMARK 465 LYS A 453 REMARK 465 LYS A 454 REMARK 465 PRO A 455 REMARK 465 PHE A 456 REMARK 465 THR A 457 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 ARG A 494 CB CG CD NE CZ NH1 NH2 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 O HOH A 768 O HOH A 838 1.72 REMARK 500 O GLY A 448 NH1 ARG A 468 1.82 REMARK 500 O HOH A 808 O HOH A 901 2.00 REMARK 500 O LEU A 108 O HOH A 701 2.03 REMARK 500 OE2 GLU A 439 O GLU A 479 2.03 REMARK 500 O PRO A 230 O HOH A 702 2.15 REMARK 500 CD1 ILE A 77 O HOH A 898 2.17 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 OG1 THR A 372 OG1 THR A 372 10665 2.00 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 MET A 458 CG MET A 458 SD 0.177 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 LEU A 37 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 ASP A 74 N - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 PRO A 101 C - N - CA ANGL. DEV. = -15.6 DEGREES REMARK 500 ARG A 214 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 PRO A 230 C - N - CD ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = -3.6 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 16 -168.11 -122.98 REMARK 500 PRO A 43 -168.82 -76.17 REMARK 500 ASP A 44 -23.71 89.83 REMARK 500 VAL A 63 -55.90 -135.51 REMARK 500 ASP A 74 14.32 -11.87 REMARK 500 ALA A 135 -56.79 167.49 REMARK 500 VAL A 180 96.96 -69.97 REMARK 500 ARG A 231 -73.09 109.66 REMARK 500 SER A 249 172.99 -55.23 REMARK 500 GLU A 294 2.22 -67.49 REMARK 500 LEU A 323 -63.03 -90.27 REMARK 500 PHE A 324 -39.39 -37.26 REMARK 500 VAL A 325 -85.99 -61.46 REMARK 500 ARG A 327 56.47 -101.54 REMARK 500 LEU A 328 -26.45 -161.12 REMARK 500 ILE A 333 -54.32 -23.95 REMARK 500 ALA A 335 34.00 -60.10 REMARK 500 ARG A 338 128.05 46.09 REMARK 500 GLU A 339 84.40 72.63 REMARK 500 ASP A 341 146.96 -178.28 REMARK 500 ASP A 348 -110.35 20.63 REMARK 500 SER A 350 -13.28 64.82 REMARK 500 SER A 402 69.91 -163.23 REMARK 500 LEU A 405 -60.03 82.15 REMARK 500 ALA A 417 42.00 -142.86 REMARK 500 SER A 426 -162.61 -178.21 REMARK 500 ARG A 429 179.03 52.82 REMARK 500 VAL A 444 -49.53 -168.88 REMARK 500 THR A 445 162.22 5.56 REMARK 500 TRP A 446 144.52 123.14 REMARK 500 MET A 458 -160.84 140.15 REMARK 500 THR A 461 145.90 151.58 REMARK 500 VAL A 478 -23.65 77.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 214 0.10 SIDE CHAIN 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 BLA A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GW9 RELATED DB: PDB REMARK 900 DIMER RESIDUES 8-635 DBREF1 5OY5 A 2 507 UNP A0A161I5N6_RHOPA DBREF2 5OY5 A A0A161I5N6 1 504 SEQADV 5OY5 MET A -19 UNP A0A161I5N INITIATING METHIONINE SEQADV 5OY5 GLY A -18 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 SER A -17 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 SER A -16 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -15 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -14 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -13 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -12 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -11 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A -10 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 SER A -9 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 SER A -8 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 GLY A -7 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 LEU A -6 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 VAL A -5 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 PRO A -4 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 ARG A -3 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 GLY A -2 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 SER A -1 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 HIS A 0 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 MET A 1 UNP A0A161I5N EXPRESSION TAG SEQADV 5OY5 VAL A 2 UNP A0A161I5N MET 1 CONFLICT SEQADV 5OY5 ILE A 291 UNP A0A161I5N MET 290 CONFLICT SEQADV 5OY5 ASP A 360 UNP A0A161I5N ALA 359 CONFLICT SEQRES 1 A 525 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 525 LEU VAL PRO ARG GLY SER HIS MET VAL ALA GLY HIS ALA SEQRES 3 A 525 SER GLY SER PRO ALA PHE GLY THR ALA ASP LEU SER ASN SEQRES 4 A 525 CYS GLU ARG GLU GLU ILE HIS LEU ALA GLY SER ILE GLN SEQRES 5 A 525 PRO HIS GLY ALA LEU LEU VAL VAL SER GLU PRO ASP HIS SEQRES 6 A 525 ARG ILE ILE GLN ALA SER ALA ASN ALA ALA GLU PHE LEU SEQRES 7 A 525 ASN LEU GLY SER VAL LEU GLY VAL PRO LEU ALA GLU ILE SEQRES 8 A 525 ASP GLY ASP LEU LEU ILE LYS ILE LEU PRO HIS LEU ASP SEQRES 9 A 525 PRO THR ALA GLU GLY MET PRO VAL ALA VAL ARG CYS ARG SEQRES 10 A 525 ILE GLY ASN PRO SER THR GLU TYR ASP GLY LEU MET HIS SEQRES 11 A 525 ARG PRO PRO GLU GLY GLY LEU ILE ILE GLU LEU GLU ARG SEQRES 12 A 525 ALA GLY PRO PRO ILE ASP LEU SER GLY THR LEU ALA PRO SEQRES 13 A 525 ALA LEU GLU ARG ILE ARG THR ALA GLY SER LEU ARG ALA SEQRES 14 A 525 LEU CYS ASP ASP THR ALA LEU LEU PHE GLN GLN CYS THR SEQRES 15 A 525 GLY TYR ASP ARG VAL MET VAL TYR ARG PHE ASP GLU GLN SEQRES 16 A 525 GLY HIS GLY GLU VAL PHE SER GLU ARG HIS VAL PRO GLY SEQRES 17 A 525 LEU GLU SER TYR PHE GLY ASN ARG TYR PRO SER SER ASP SEQRES 18 A 525 ILE PRO GLN MET ALA ARG ARG LEU TYR GLU ARG GLN ARG SEQRES 19 A 525 VAL ARG VAL LEU VAL ASP VAL SER TYR GLN PRO VAL PRO SEQRES 20 A 525 LEU GLU PRO ARG LEU SER PRO LEU THR GLY ARG ASP LEU SEQRES 21 A 525 ASP MET SER GLY CYS PHE LEU ARG SER MET SER PRO ILE SEQRES 22 A 525 HIS LEU GLN TYR LEU LYS ASN MET GLY VAL ARG ALA THR SEQRES 23 A 525 LEU VAL VAL SER LEU VAL VAL GLY GLY LYS LEU TRP GLY SEQRES 24 A 525 LEU VAL ALA CYS HIS HIS TYR LEU PRO ARG PHE ILE HIS SEQRES 25 A 525 PHE GLU LEU ARG ALA ILE CYS GLU LEU LEU ALA GLU ALA SEQRES 26 A 525 ILE ALA THR ARG ILE THR ALA LEU GLU SER PHE ALA GLN SEQRES 27 A 525 SER GLN SER GLU LEU PHE VAL GLN ARG LEU GLU GLN ARG SEQRES 28 A 525 MET ILE GLU ALA ILE THR ARG GLU GLY ASP TRP ARG ALA SEQRES 29 A 525 ALA ILE PHE ASP THR SER GLN SER ILE LEU GLN PRO LEU SEQRES 30 A 525 HIS ALA ASP GLY CYS ALA LEU VAL TYR GLU ASP GLN ILE SEQRES 31 A 525 ARG THR ILE GLY ASP VAL PRO SER THR GLN ASP VAL ARG SEQRES 32 A 525 GLU ILE ALA GLY TRP LEU ASP ARG GLN PRO ARG ALA ALA SEQRES 33 A 525 VAL THR SER THR ALA SER LEU GLY LEU ASP VAL PRO GLU SEQRES 34 A 525 LEU ALA HIS LEU THR ARG MET ALA SER GLY VAL VAL ALA SEQRES 35 A 525 ALA PRO ILE SER ASP HIS ARG GLY GLU PHE LEU MET TRP SEQRES 36 A 525 PHE ARG PRO GLU ARG VAL HIS THR VAL THR TRP GLY GLY SEQRES 37 A 525 ASP PRO LYS LYS PRO PHE THR MET GLY ASP THR PRO ALA SEQRES 38 A 525 ASP LEU SER PRO ARG ARG SER PHE ALA LYS TRP HIS GLN SEQRES 39 A 525 VAL VAL GLU GLY THR SER ASP PRO TRP THR ALA ALA ASP SEQRES 40 A 525 LEU ALA ALA ALA ARG THR ILE GLY GLN THR VAL ALA ASP SEQRES 41 A 525 ILE VAL LEU GLN PHE HET BLA A 600 43 HETNAM BLA BILIVERDINE IX ALPHA FORMUL 2 BLA C33 H34 N4 O6 FORMUL 3 HOH *218(H2 O) HELIX 1 AA1 ASN A 19 GLU A 23 5 5 HELIX 2 AA2 GLU A 24 ALA A 28 5 5 HELIX 3 AA3 ASN A 53 ASN A 59 1 7 HELIX 4 AA4 PRO A 67 ILE A 71 5 5 HELIX 5 AA5 ASP A 74 LEU A 80 1 7 HELIX 6 AA6 PRO A 81 ASP A 84 5 4 HELIX 7 AA7 ALA A 135 THR A 143 1 9 HELIX 8 AA8 SER A 146 GLY A 163 1 18 HELIX 9 AA9 PRO A 198 ILE A 202 5 5 HELIX 10 AB1 PRO A 203 GLN A 213 1 11 HELIX 11 AB2 SER A 251 MET A 261 1 11 HELIX 12 AB3 GLU A 294 ARG A 327 1 34 HELIX 13 AB4 LEU A 328 GLU A 334 1 7 HELIX 14 AB5 TRP A 342 PHE A 347 1 6 HELIX 15 AB6 LEU A 354 HIS A 358 5 5 HELIX 16 AB7 SER A 378 ASP A 390 1 13 HELIX 17 AB8 SER A 402 VAL A 407 1 6 HELIX 18 AB9 PRO A 408 HIS A 412 5 5 HELIX 19 AC1 LEU A 413 SER A 418 1 6 HELIX 20 AC2 GLU A 439 VAL A 444 5 6 HELIX 21 AC3 THR A 461 LEU A 465 5 5 HELIX 22 AC4 SER A 466 VAL A 477 1 12 HELIX 23 AC5 THR A 486 PHE A 507 1 22 SHEET 1 AA1 7 SER A 30 ILE A 31 0 SHEET 2 AA1 7 VAL A 226 GLU A 229 -1 O VAL A 226 N ILE A 31 SHEET 3 AA1 7 ILE A 47 SER A 51 -1 N ALA A 50 O GLU A 229 SHEET 4 AA1 7 ALA A 36 VAL A 40 -1 N LEU A 37 O SER A 51 SHEET 5 AA1 7 LEU A 117 ARG A 123 -1 O LEU A 117 N VAL A 40 SHEET 6 AA1 7 THR A 103 HIS A 110 -1 N LEU A 108 O GLU A 120 SHEET 7 AA1 7 VAL A 92 ILE A 98 -1 N VAL A 94 O GLY A 107 SHEET 1 AA2 6 ARG A 196 TYR A 197 0 SHEET 2 AA2 6 GLY A 178 HIS A 185 -1 N GLY A 178 O TYR A 197 SHEET 3 AA2 6 ARG A 166 PHE A 172 -1 N VAL A 167 O ARG A 184 SHEET 4 AA2 6 LYS A 276 HIS A 285 -1 O ALA A 282 N MET A 168 SHEET 5 AA2 6 ALA A 265 VAL A 273 -1 N VAL A 269 O VAL A 281 SHEET 6 AA2 6 VAL A 215 LEU A 218 -1 N ARG A 216 O VAL A 268 SHEET 1 AA3 5 GLN A 369 GLY A 374 0 SHEET 2 AA3 5 GLY A 361 TYR A 366 -1 N CYS A 362 O ILE A 373 SHEET 3 AA3 5 PHE A 432 ARG A 437 -1 O PHE A 436 N GLY A 361 SHEET 4 AA3 5 GLY A 419 PRO A 424 -1 N VAL A 421 O TRP A 435 SHEET 5 AA3 5 THR A 398 THR A 400 -1 N THR A 398 O ALA A 422 LINK SG CYS A 20 CBC BLA A 600 1555 1555 1.67 CISPEP 1 GLU A 42 PRO A 43 0 -9.61 CISPEP 2 MET A 90 PRO A 91 0 -0.97 CISPEP 3 GLU A 229 PRO A 230 0 14.33 SITE 1 AC1 24 CYS A 20 TYR A 170 TYR A 197 ASP A 201 SITE 2 AC1 24 ILE A 202 PRO A 203 TYR A 210 ARG A 216 SITE 3 AC1 24 MET A 250 SER A 251 ILE A 253 HIS A 254 SITE 4 AC1 24 TYR A 257 ALA A 282 HIS A 284 PRO A 467 SITE 5 AC1 24 SER A 470 HOH A 708 HOH A 709 HOH A 712 SITE 6 AC1 24 HOH A 734 HOH A 738 HOH A 754 HOH A 775 CRYST1 92.780 92.780 449.170 90.00 90.00 120.00 P 65 2 2 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 0.010778 0.006223 0.000000 0.00000 SCALE2 0.000000 0.012446 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002226 0.00000