HEADER OXIDOREDUCTASE 13-JAN-17 5UIB TITLE CRYSTAL STRUCTURE OF AN OXIDOREDUCTASE FROM AGROBACTERIUM RADIOBACTER TITLE 2 IN COMPLEX WITH NAD+, L-TARTARIC ACID AND MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXIDOREDUCTASE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM RADIOBACTER (STRAIN K84 / ATCC SOURCE 3 BAA-868); SOURCE 4 ORGANISM_TAXID: 311403; SOURCE 5 STRAIN: K84 / ATCC BAA-868; SOURCE 6 GENE: ARAD_9238; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, L-TARTRATE EXPDTA X-RAY DIFFRACTION AUTHOR W.J.COOK,A.A.FEDOROV,E.V.FEDOROV,H.HUANG,J.B.BONANNO,J.A.GERLT, AUTHOR 2 S.C.ALMO REVDAT 5 04-OCT-23 5UIB 1 REMARK REVDAT 4 01-JAN-20 5UIB 1 REMARK REVDAT 3 20-SEP-17 5UIB 1 REMARK REVDAT 2 07-JUN-17 5UIB 1 AUTHOR REVDAT 1 25-JAN-17 5UIB 0 JRNL AUTH W.J.COOK,A.A.FEDOROV,E.V.FEDOROV,H.HUANG,J.B.BONANNO, JRNL AUTH 2 J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF AN OXIDOREDUCTASE FROM AGROBACTERIUM JRNL TITL 2 RADIOBACTER IN COMPLEX WITH NAD+, L-TARTARIC ACID AND JRNL TITL 3 MAGNESIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27812 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2028 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : -0.71000 REMARK 3 B33 (A**2) : 1.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.497 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.282 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.263 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.189 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5407 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4933 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7351 ; 1.268 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11405 ; 0.900 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 682 ; 6.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;36.364 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 844 ;14.303 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;14.789 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 832 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6053 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1130 ; 0.001 ; 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): 2734 ; 0.712 ; 3.526 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2733 ; 0.712 ; 3.525 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3414 ; 1.257 ; 5.286 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3415 ; 1.257 ; 5.287 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2673 ; 0.607 ; 3.656 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2670 ; 0.606 ; 3.655 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3936 ; 1.080 ; 5.461 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5926 ; 2.517 ;42.186 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5926 ; 2.517 ;42.186 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 4 A 345 REMARK 3 ORIGIN FOR THE GROUP (A): 18.1087 -30.9534 15.3320 REMARK 3 T TENSOR REMARK 3 T11: 0.2188 T22: 0.2972 REMARK 3 T33: 0.0130 T12: -0.0742 REMARK 3 T13: 0.0417 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.8004 L22: 1.3347 REMARK 3 L33: 1.4113 L12: 0.0830 REMARK 3 L13: -0.1531 L23: 0.5416 REMARK 3 S TENSOR REMARK 3 S11: 0.1341 S12: -0.0735 S13: 0.0353 REMARK 3 S21: 0.2156 S22: -0.1574 S23: -0.0257 REMARK 3 S31: 0.2032 S32: -0.0267 S33: 0.0233 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 4 B 345 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2782 -55.9111 -19.7694 REMARK 3 T TENSOR REMARK 3 T11: 0.2402 T22: 0.3587 REMARK 3 T33: 0.0114 T12: 0.0860 REMARK 3 T13: 0.0097 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 0.4478 L22: 1.6577 REMARK 3 L33: 0.5457 L12: -0.5883 REMARK 3 L13: -0.2347 L23: 0.4308 REMARK 3 S TENSOR REMARK 3 S11: 0.1943 S12: 0.1830 S13: -0.0291 REMARK 3 S21: -0.0681 S22: -0.2241 S23: 0.0026 REMARK 3 S31: 0.0369 S32: -0.0818 S33: 0.0298 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5UIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DIAMOND 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 : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 29.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.82700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5UHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, 5 MM NAD+, 5 MM REMARK 280 MAGNESIUM CHLORIDE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.31100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.55450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.31100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 56.55450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 ASN A 2 REMARK 465 MET A 3 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 MET B 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 147 CD OE1 OE2 REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 269 CG OD1 ND2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 ARG B 112 CD NE CZ NH1 NH2 REMARK 470 LYS B 209 CG CD CE NZ REMARK 470 ARG B 337 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 174 -92.65 -140.62 REMARK 500 PRO A 242 54.93 -116.69 REMARK 500 THR A 314 60.91 -105.01 REMARK 500 CYS B 13 50.68 -97.17 REMARK 500 PHE B 174 -85.33 -118.57 REMARK 500 PRO B 242 56.76 -109.83 REMARK 500 ASN B 269 51.22 -99.85 REMARK 500 THR B 314 54.15 -106.12 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 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 24 O REMARK 620 2 LYS A 25 O 74.7 REMARK 620 3 VAL A 27 O 83.7 91.3 REMARK 620 4 ALA A 30 O 76.6 149.2 74.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 24 O REMARK 620 2 LYS B 25 O 73.9 REMARK 620 3 ALA B 30 O 82.9 151.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UHW RELATED DB: PDB REMARK 900 5UHW CONTAINS THE SAME PROTEIN WITHOUT L-TARTARIC ACID REMARK 900 RELATED ID: 5UHZ RELATED DB: PDB REMARK 900 RELATED ID: 5UI9 RELATED DB: PDB REMARK 900 RELATED ID: 5UIA RELATED DB: PDB DBREF 5UIB A 1 345 UNP B9JK80 B9JK80_AGRRK 1 345 DBREF 5UIB B 1 345 UNP B9JK80 B9JK80_AGRRK 1 345 SEQRES 1 A 345 MET ASN MET THR GLU LEU LYS GLY ALA LEU ILE GLY CYS SEQRES 2 A 345 GLY PHE PHE ALA VAL ASN GLN MET HIS ALA TRP LYS ASP SEQRES 3 A 345 VAL LYS GLY ALA GLY ILE ALA ALA ILE CYS ASP ARG ASP SEQRES 4 A 345 PRO LYS ARG LEU LYS LEU VAL GLY ASP GLN PHE GLY ILE SEQRES 5 A 345 GLU ARG ARG TYR GLY ASP ALA ALA ALA LEU PHE ALA ASP SEQRES 6 A 345 GLY GLY PHE ASP PHE VAL ASP ILE ALA THR THR VAL GLN SEQRES 7 A 345 SER HIS ARG ALA LEU VAL GLU MET ALA ALA ALA HIS LYS SEQRES 8 A 345 VAL PRO ALA ILE CYS GLN LYS PRO PHE ALA LYS SER LEU SEQRES 9 A 345 SER ASP ALA LYS ALA MET VAL ARG THR CYS GLU ASN ALA SEQRES 10 A 345 ASP ILE PRO LEU MET VAL HIS GLU ASN PHE ARG TRP GLN SEQRES 11 A 345 THR PRO ILE GLN ALA VAL LYS ALA VAL LEU GLU SER GLY SEQRES 12 A 345 ALA ILE GLY GLU PRO PHE TRP GLY ARG PHE SER PHE ARG SEQRES 13 A 345 SER GLY PHE ASP VAL PHE SER GLY GLN PRO TYR LEU ALA SEQRES 14 A 345 GLU GLY GLU ARG PHE ILE ILE GLU ASP LEU GLY ILE HIS SEQRES 15 A 345 THR LEU ASP ILE ALA ARG PHE ILE LEU GLY ASP VAL ALA SEQRES 16 A 345 THR LEU THR ALA ARG THR LYS ARG VAL ASN PRO LYS ILE SEQRES 17 A 345 LYS GLY GLU ASP VAL ALA THR ILE LEU LEU ASP HIS GLN SEQRES 18 A 345 ASN GLY ALA THR SER ILE VAL ASP VAL SER TYR ALA THR SEQRES 19 A 345 LYS LEU GLY THR GLU PRO PHE PRO GLU THR LEU ILE ASP SEQRES 20 A 345 ILE ASP GLY THR GLN GLY THR ILE ARG LEU SER GLN GLY SEQRES 21 A 345 TYR ARG LEU GLU VAL THR GLY PRO ASN GLY MET THR ILE SEQRES 22 A 345 SER ASP ALA SER PRO GLN LEU LEU SER TRP ALA SER ARG SEQRES 23 A 345 PRO TRP HIS ASN ILE GLN GLU SER VAL LEU ALA ILE GLN SEQRES 24 A 345 GLN HIS TRP THR ASP ARG LEU SER SER GLY GLY GLU THR SEQRES 25 A 345 SER THR SER GLY ALA ASP ASN LEU LYS THR PHE ALA LEU SEQRES 26 A 345 VAL GLU ALA ALA TYR GLU SER ALA ALA ASN GLY ARG THR SEQRES 27 A 345 VAL ASP ILE GLY ALA MET LEU SEQRES 1 B 345 MET ASN MET THR GLU LEU LYS GLY ALA LEU ILE GLY CYS SEQRES 2 B 345 GLY PHE PHE ALA VAL ASN GLN MET HIS ALA TRP LYS ASP SEQRES 3 B 345 VAL LYS GLY ALA GLY ILE ALA ALA ILE CYS ASP ARG ASP SEQRES 4 B 345 PRO LYS ARG LEU LYS LEU VAL GLY ASP GLN PHE GLY ILE SEQRES 5 B 345 GLU ARG ARG TYR GLY ASP ALA ALA ALA LEU PHE ALA ASP SEQRES 6 B 345 GLY GLY PHE ASP PHE VAL ASP ILE ALA THR THR VAL GLN SEQRES 7 B 345 SER HIS ARG ALA LEU VAL GLU MET ALA ALA ALA HIS LYS SEQRES 8 B 345 VAL PRO ALA ILE CYS GLN LYS PRO PHE ALA LYS SER LEU SEQRES 9 B 345 SER ASP ALA LYS ALA MET VAL ARG THR CYS GLU ASN ALA SEQRES 10 B 345 ASP ILE PRO LEU MET VAL HIS GLU ASN PHE ARG TRP GLN SEQRES 11 B 345 THR PRO ILE GLN ALA VAL LYS ALA VAL LEU GLU SER GLY SEQRES 12 B 345 ALA ILE GLY GLU PRO PHE TRP GLY ARG PHE SER PHE ARG SEQRES 13 B 345 SER GLY PHE ASP VAL PHE SER GLY GLN PRO TYR LEU ALA SEQRES 14 B 345 GLU GLY GLU ARG PHE ILE ILE GLU ASP LEU GLY ILE HIS SEQRES 15 B 345 THR LEU ASP ILE ALA ARG PHE ILE LEU GLY ASP VAL ALA SEQRES 16 B 345 THR LEU THR ALA ARG THR LYS ARG VAL ASN PRO LYS ILE SEQRES 17 B 345 LYS GLY GLU ASP VAL ALA THR ILE LEU LEU ASP HIS GLN SEQRES 18 B 345 ASN GLY ALA THR SER ILE VAL ASP VAL SER TYR ALA THR SEQRES 19 B 345 LYS LEU GLY THR GLU PRO PHE PRO GLU THR LEU ILE ASP SEQRES 20 B 345 ILE ASP GLY THR GLN GLY THR ILE ARG LEU SER GLN GLY SEQRES 21 B 345 TYR ARG LEU GLU VAL THR GLY PRO ASN GLY MET THR ILE SEQRES 22 B 345 SER ASP ALA SER PRO GLN LEU LEU SER TRP ALA SER ARG SEQRES 23 B 345 PRO TRP HIS ASN ILE GLN GLU SER VAL LEU ALA ILE GLN SEQRES 24 B 345 GLN HIS TRP THR ASP ARG LEU SER SER GLY GLY GLU THR SEQRES 25 B 345 SER THR SER GLY ALA ASP ASN LEU LYS THR PHE ALA LEU SEQRES 26 B 345 VAL GLU ALA ALA TYR GLU SER ALA ALA ASN GLY ARG THR SEQRES 27 B 345 VAL ASP ILE GLY ALA MET LEU HET NAD A 401 44 HET TLA A 402 10 HET MG A 403 1 HET NAD B 401 44 HET TLA B 402 10 HET MG B 403 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM TLA L(+)-TARTARIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 TLA 2(C4 H6 O6) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *22(H2 O) HELIX 1 AA1 PHE A 16 VAL A 27 1 12 HELIX 2 AA2 ASP A 39 PHE A 50 1 12 HELIX 3 AA3 ASP A 58 GLY A 66 1 9 HELIX 4 AA4 THR A 76 HIS A 90 1 15 HELIX 5 AA5 SER A 103 ALA A 117 1 15 HELIX 6 AA6 ASN A 126 TRP A 129 5 4 HELIX 7 AA7 GLN A 130 GLY A 143 1 14 HELIX 8 AA8 GLN A 165 GLU A 170 5 6 HELIX 9 AA9 PHE A 174 LEU A 179 1 6 HELIX 10 AB1 LEU A 179 GLY A 192 1 14 HELIX 11 AB2 TRP A 288 GLY A 309 1 22 HELIX 12 AB3 SER A 315 GLY A 336 1 22 HELIX 13 AB4 ILE A 341 LEU A 345 1 5 HELIX 14 AB5 PHE B 16 VAL B 27 1 12 HELIX 15 AB6 ASP B 39 PHE B 50 1 12 HELIX 16 AB7 ASP B 58 GLY B 66 1 9 HELIX 17 AB8 THR B 76 GLN B 78 5 3 HELIX 18 AB9 SER B 79 HIS B 90 1 12 HELIX 19 AC1 SER B 103 ASP B 118 1 16 HELIX 20 AC2 ASN B 126 TRP B 129 5 4 HELIX 21 AC3 GLN B 130 GLY B 143 1 14 HELIX 22 AC4 PRO B 166 GLY B 171 1 6 HELIX 23 AC5 PHE B 174 LEU B 179 1 6 HELIX 24 AC6 LEU B 179 GLY B 192 1 14 HELIX 25 AC7 TRP B 288 GLY B 309 1 22 HELIX 26 AC8 SER B 315 GLY B 336 1 22 HELIX 27 AC9 ILE B 341 LEU B 345 1 5 SHEET 1 AA1 6 ARG A 54 TYR A 56 0 SHEET 2 AA1 6 ALA A 30 CYS A 36 1 N ILE A 35 O TYR A 56 SHEET 3 AA1 6 LEU A 6 ILE A 11 1 N GLY A 8 O GLY A 31 SHEET 4 AA1 6 PHE A 70 ILE A 73 1 O ASP A 72 N ALA A 9 SHEET 5 AA1 6 ALA A 94 CYS A 96 1 O ILE A 95 N ILE A 73 SHEET 6 AA1 6 LEU A 121 VAL A 123 1 O MET A 122 N CYS A 96 SHEET 1 AA2 9 MET A 271 ASP A 275 0 SHEET 2 AA2 9 ARG A 262 THR A 266 -1 N LEU A 263 O SER A 274 SHEET 3 AA2 9 GLY A 253 SER A 258 -1 N SER A 258 O ARG A 262 SHEET 4 AA2 9 LEU A 245 GLY A 250 -1 N GLY A 250 O GLY A 253 SHEET 5 AA2 9 PRO A 148 ARG A 156 -1 N SER A 154 O LEU A 245 SHEET 6 AA2 9 THR A 225 SER A 231 1 O ILE A 227 N PHE A 153 SHEET 7 AA2 9 VAL A 213 HIS A 220 -1 N ILE A 216 O VAL A 228 SHEET 8 AA2 9 VAL A 194 LYS A 202 -1 N THR A 198 O LEU A 217 SHEET 9 AA2 9 VAL A 339 ASP A 340 -1 O VAL A 339 N LEU A 197 SHEET 1 AA3 6 ARG B 54 TYR B 56 0 SHEET 2 AA3 6 ALA B 30 CYS B 36 1 N ILE B 35 O ARG B 54 SHEET 3 AA3 6 LEU B 6 ILE B 11 1 N LEU B 10 O CYS B 36 SHEET 4 AA3 6 PHE B 70 ILE B 73 1 O ASP B 72 N ALA B 9 SHEET 5 AA3 6 ALA B 94 GLN B 97 1 O ILE B 95 N ILE B 73 SHEET 6 AA3 6 LEU B 121 HIS B 124 1 O HIS B 124 N CYS B 96 SHEET 1 AA4 9 GLY B 270 ASP B 275 0 SHEET 2 AA4 9 ARG B 262 GLY B 267 -1 N LEU B 263 O SER B 274 SHEET 3 AA4 9 THR B 254 SER B 258 -1 N SER B 258 O ARG B 262 SHEET 4 AA4 9 LEU B 245 GLY B 250 -1 N ILE B 246 O LEU B 257 SHEET 5 AA4 9 PRO B 148 ARG B 156 -1 N PHE B 149 O ASP B 249 SHEET 6 AA4 9 THR B 225 SER B 231 1 O ILE B 227 N PHE B 153 SHEET 7 AA4 9 VAL B 213 HIS B 220 -1 N ILE B 216 O VAL B 228 SHEET 8 AA4 9 VAL B 194 LYS B 202 -1 N THR B 196 O ASP B 219 SHEET 9 AA4 9 VAL B 339 ASP B 340 -1 O VAL B 339 N LEU B 197 LINK O TRP A 24 MG MG A 403 1555 1555 2.72 LINK O LYS A 25 MG MG A 403 1555 1555 2.79 LINK O VAL A 27 MG MG A 403 1555 1555 2.62 LINK O ALA A 30 MG MG A 403 1555 1555 2.60 LINK O TRP B 24 MG MG B 403 1555 1555 2.48 LINK O LYS B 25 MG MG B 403 1555 1555 2.89 LINK O ALA B 30 MG MG B 403 1555 1555 2.33 CISPEP 1 LYS A 98 PRO A 99 0 -10.49 CISPEP 2 PHE A 241 PRO A 242 0 8.30 CISPEP 3 ARG A 286 PRO A 287 0 1.53 CISPEP 4 LYS B 98 PRO B 99 0 -16.94 CISPEP 5 PHE B 241 PRO B 242 0 -2.77 CISPEP 6 ARG B 286 PRO B 287 0 3.09 SITE 1 AC1 22 ILE A 11 GLY A 12 GLY A 14 PHE A 15 SITE 2 AC1 22 PHE A 16 ASP A 37 ARG A 38 ASP A 39 SITE 3 AC1 22 ALA A 74 THR A 75 THR A 76 SER A 79 SITE 4 AC1 22 GLN A 97 LYS A 98 PRO A 99 ASN A 126 SITE 5 AC1 22 GLN A 165 TYR A 167 HIS A 182 TLA A 402 SITE 6 AC1 22 HOH A 501 HOH A 510 SITE 1 AC2 8 LYS A 98 VAL A 161 GLN A 165 ASP A 178 SITE 2 AC2 8 LEU A 179 HIS A 182 TYR A 232 NAD A 401 SITE 1 AC3 4 TRP A 24 LYS A 25 VAL A 27 ALA A 30 SITE 1 AC4 18 GLY B 12 GLY B 14 PHE B 15 PHE B 16 SITE 2 AC4 18 ASP B 37 ARG B 38 THR B 75 THR B 76 SITE 3 AC4 18 SER B 79 GLN B 97 LYS B 98 PRO B 99 SITE 4 AC4 18 ASN B 126 GLN B 165 TYR B 167 ILE B 291 SITE 5 AC4 18 TLA B 402 HOH B 502 SITE 1 AC5 10 LYS B 98 PHE B 127 VAL B 161 GLN B 165 SITE 2 AC5 10 ASP B 178 LEU B 179 HIS B 182 TYR B 232 SITE 3 AC5 10 ILE B 291 NAD B 401 SITE 1 AC6 4 TRP B 24 LYS B 25 VAL B 27 ALA B 30 CRYST1 138.622 113.109 65.820 90.00 94.61 90.00 C 1 2 1 8 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 0.007214 0.000000 0.000581 0.00000 SCALE2 0.000000 0.008841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015242 0.00000