HEADER OXIDOREDUCTASE 09-DEC-14 4X7G TITLE COBK PRECORRIN-6A REDUCTASE CAVEAT 4X7G 3Y8 A 302 HAS WRONG CHIRALITY AT ATOM C8 3Y8 A 302 HAS WRONG CAVEAT 2 4X7G CHIRALITY AT ATOM C6 3Y8 A 302 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 4X7G C16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRECORRIN-6A REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PRECORRIN-6X REDUCTASE; COMPND 5 EC: 1.3.1.54; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS (STRAIN ATCC BAA-309 / SOURCE 3 NBRC 16581 / SB1003); SOURCE 4 ORGANISM_TAXID: 272942; SOURCE 5 ATCC: BAA-309; SOURCE 6 GENE: COBK, RCAP_RCC02043; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS OXIDOREDUCTASE, NADP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.GU,E.DEERY,M.J.WARREN,R.W.PICKERSGILL REVDAT 3 23-OCT-24 4X7G 1 REMARK REVDAT 2 30-AUG-17 4X7G 1 REMARK REVDAT 1 20-JAN-16 4X7G 0 JRNL AUTH S.GU,O.SUSHKO,E.DEERY,M.J.WARREN,R.W.PICKERSGILL JRNL TITL CRYSTAL STRUCTURE OF COBK REVEALS STRAND-SWAPPING BETWEEN JRNL TITL 2 ROSSMANN-FOLD DOMAINS AND MOLECULAR BASIS OF THE REDUCED JRNL TITL 3 PRECORRIN PRODUCT TRAP. JRNL REF SCI REP V. 5 16943 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26616290 JRNL DOI 10.1038/SREP16943 REMARK 2 REMARK 2 RESOLUTION. 1.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 69845 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3676 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) : 1.22 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5115 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 269 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1836 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 186 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.041 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.719 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2043 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1948 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2826 ; 2.831 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4467 ; 1.451 ; 3.010 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.615 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;32.052 ;22.267 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 268 ;11.982 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.541 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 323 ; 0.311 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2311 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 452 ; 0.002 ; 0.020 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): 1018 ; 1.487 ; 1.417 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1017 ; 1.442 ; 1.416 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1275 ; 2.061 ; 2.132 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1276 ; 2.061 ; 2.133 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1025 ; 3.190 ; 1.657 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1023 ; 3.192 ; 1.657 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1546 ; 3.955 ; 2.399 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2416 ; 5.532 ;12.814 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2417 ; 5.531 ;12.815 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 : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4X7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : AIMLESS, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73880 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 47.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.090 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2540 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.59600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% W/V PEG 3350, 0.2 M NH4 CL, PH REMARK 280 8.0, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 26.54500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.12500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.12500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.14000 REMARK 290 SMTRY3 4 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 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: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 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 26 CD GLU A 26 OE2 -0.078 REMARK 500 TYR A 59 CZ TYR A 59 CE2 -0.098 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 MSE A 1 CA - C - N ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 22 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 46 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 46 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP A 115 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 115 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 168 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 173 CG - CD - NE ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 221 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 243 CB - CG - OD1 ANGL. DEV. = 6.1 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 159 -67.82 -99.36 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 NAP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3Y8 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5C4R RELATED DB: PDB DBREF 4X7G A 2 251 UNP O68098 COBK_RHOCB 2 251 SEQADV 4X7G MSE A 1 UNP O68098 INITIATING METHIONINE SEQRES 1 A 251 MSE THR ARG LEU LEU VAL LEU GLY GLY THR THR GLU ALA SEQRES 2 A 251 SER ARG LEU ALA LYS THR LEU ALA ASP GLN GLY PHE GLU SEQRES 3 A 251 ALA VAL PHE SER TYR ALA GLY ARG THR GLY ALA PRO VAL SEQRES 4 A 251 ALA GLN PRO LEU PRO THR ARG ILE GLY GLY PHE GLY GLY SEQRES 5 A 251 VAL ALA GLY LEU VAL ASP TYR LEU THR ARG GLU GLY VAL SEQRES 6 A 251 SER HIS VAL ILE ASP ALA THR HIS PRO PHE ALA ALA GLN SEQRES 7 A 251 MSE SER ALA ASN ALA VAL ALA ALA CYS ALA GLN THR GLY SEQRES 8 A 251 VAL ALA LEU CYS ALA PHE GLU ARG ALA PRO TRP THR ALA SEQRES 9 A 251 GLN ALA GLY ASP ARG TRP THR HIS VAL PRO ASP LEU ALA SEQRES 10 A 251 ALA ALA VAL ALA ALA LEU PRO GLN ALA PRO ALA ARG VAL SEQRES 11 A 251 PHE LEU ALA ILE GLY LYS GLN HIS LEU ARG ASP PHE SER SEQRES 12 A 251 ALA ALA PRO GLN HIS HIS TYR LEU LEU ARG LEU VAL ASP SEQRES 13 A 251 PRO PRO GLU GLY PRO LEU PRO LEU PRO ASP ALA ARG ALA SEQRES 14 A 251 VAL ILE ALA ARG GLY PRO PHE THR VAL GLN GLY ASP THR SEQRES 15 A 251 GLU LEU LEU ARG SER GLU THR ILE THR HIS VAL VAL ALA SEQRES 16 A 251 LYS ASN ALA GLY GLY ALA GLY ALA GLU ALA LYS LEU ILE SEQRES 17 A 251 ALA ALA ARG SER LEU GLY LEU PRO VAL ILE LEU ILE ASP SEQRES 18 A 251 ARG PRO ALA VAL PRO ALA ARG ASP ILE CYS ALA THR LEU SEQRES 19 A 251 GLU GLY VAL MSE GLY TRP LEU ALA ASP HIS GLY ALA THR SEQRES 20 A 251 PRO ARG GLY VAL MODRES 4X7G MSE A 79 MET MODIFIED RESIDUE MODRES 4X7G MSE A 238 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 79 8 HET MSE A 238 16 HET NAP A 301 48 HET 3Y8 A 302 65 HETNAM MSE SELENOMETHIONINE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM 3Y8 3-[(1R,2S,3S,7S,11S,16S,17R,18R,19R)-2,7,12,18- HETNAM 2 3Y8 TETRAKIS(2-HYDROXY-2-OXOETHYL)-3,13-BIS(3-HYDROXY-3- HETNAM 3 3Y8 OXOPROPYL)-1,2,5,7,11,17-HEXAMETHYL-17-(3-OXIDANYL-3- HETNAM 4 3Y8 OXIDANYLIDENE-PROP-1-ENYL)-3,6,8,10,15,16,18,19,21,24- HETNAM 5 3Y8 DECAHYDROCORRIN-8-YL]PROPANOIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 3Y8 C45 H60 N4 O16 FORMUL 4 HOH *186(H2 O) HELIX 1 AA1 THR A 10 GLN A 23 1 14 HELIX 2 AA2 GLY A 51 GLY A 64 1 14 HELIX 3 AA3 ALA A 76 GLY A 91 1 16 HELIX 4 AA4 ASP A 115 LEU A 123 1 9 HELIX 5 AA5 HIS A 138 ALA A 145 5 8 HELIX 6 AA6 THR A 177 GLU A 188 1 12 HELIX 7 AA7 GLU A 204 LEU A 213 1 10 HELIX 8 AA8 THR A 233 HIS A 244 1 12 SHEET 1 AA1 6 THR A 45 ILE A 47 0 SHEET 2 AA1 6 ALA A 27 TYR A 31 1 N PHE A 29 O ARG A 46 SHEET 3 AA1 6 LEU A 4 LEU A 7 1 N VAL A 6 O VAL A 28 SHEET 4 AA1 6 HIS A 67 ASP A 70 1 O ILE A 69 N LEU A 5 SHEET 5 AA1 6 ALA A 93 PHE A 97 1 O ALA A 93 N VAL A 68 SHEET 6 AA1 6 ASP A 229 CYS A 231 1 O CYS A 231 N ALA A 96 SHEET 1 AA2 6 ARG A 109 VAL A 113 0 SHEET 2 AA2 6 PRO A 216 ILE A 220 1 O LEU A 219 N THR A 111 SHEET 3 AA2 6 HIS A 192 LYS A 196 1 N VAL A 193 O ILE A 218 SHEET 4 AA2 6 ARG A 129 LEU A 132 1 N PHE A 131 O VAL A 194 SHEET 5 AA2 6 HIS A 149 LEU A 154 1 O HIS A 149 N VAL A 130 SHEET 6 AA2 6 ALA A 167 ILE A 171 1 O VAL A 170 N LEU A 152 SSBOND 1 CYS A 95 CYS A 231 1555 1555 2.01 LINK C MSE A 1 N THR A 2 1555 1555 1.25 LINK C GLN A 78 N MSE A 79 1555 1555 1.35 LINK C MSE A 79 N SER A 80 1555 1555 1.32 LINK C VAL A 237 N AMSE A 238 1555 1555 1.33 LINK C VAL A 237 N BMSE A 238 1555 1555 1.33 LINK C AMSE A 238 N GLY A 239 1555 1555 1.34 LINK C BMSE A 238 N GLY A 239 1555 1555 1.33 CISPEP 1 GLY A 174 PRO A 175 0 6.96 SITE 1 AC1 25 GLY A 8 GLY A 9 SER A 30 TYR A 31 SITE 2 AC1 25 ALA A 32 ARG A 34 GLY A 48 GLY A 49 SITE 3 AC1 25 PHE A 50 GLY A 51 GLY A 52A THR A 72 SITE 4 AC1 25 HIS A 73 ALA A 76 ALA A 77 GLN A 78 SITE 5 AC1 25 MSE A 79 ASN A 82 GLN A 137 LYS A 196 SITE 6 AC1 25 3Y8 A 302 HOH A 409 HOH A 426 HOH A 498 SITE 7 AC1 25 HOH A 516 SITE 1 AC2 40 GLY A 9 THR A 10 THR A 11 SER A 14 SITE 2 AC2 40 TYR A 31 ALA A 32 GLY A 33 ARG A 34 SITE 3 AC2 40 THR A 35 PRO A 38 VAL A 39 HIS A 73 SITE 4 AC2 40 ALA A 133 ILE A 134 GLY A 135 LYS A 136 SITE 5 AC2 40 GLN A 137 ARG A 153 VAL A 155 ARG A 173 SITE 6 AC2 40 GLY A 174 PRO A 175 LYS A 196 ALA A 203 SITE 7 AC2 40 LYS A 206 NAP A 301 HOH A 404 HOH A 407 SITE 8 AC2 40 HOH A 413 HOH A 418 HOH A 431 HOH A 435 SITE 9 AC2 40 HOH A 436 HOH A 443 HOH A 455 HOH A 456 SITE 10 AC2 40 HOH A 475 HOH A 479 HOH A 486 HOH A 556 CRYST1 53.090 60.280 76.250 90.00 90.00 90.00 P 21 21 21 4 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 0.018836 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013115 0.00000 HETATM 1 N MSE A 1 12.278 2.600 -3.710 1.00 26.35 N HETATM 2 CA MSE A 1 13.076 1.374 -3.958 1.00 29.30 C HETATM 3 C MSE A 1 14.570 1.475 -3.558 1.00 18.63 C HETATM 4 O MSE A 1 15.178 2.492 -3.203 1.00 19.84 O HETATM 5 CB MSE A 1 12.994 1.026 -5.444 1.00 20.00 C HETATM 6 CG MSE A 1 11.601 0.624 -5.899 1.00 20.00 C HETATM 7 SE MSE A 1 10.886 -0.915 -5.005 1.00 20.00 SE HETATM 8 CE MSE A 1 12.125 -2.246 -5.710 1.00 20.00 C