HEADER OXIDOREDUCTASE 13-JAN-17 5UIA TITLE CRYSTAL STRUCTURE OF AN OXIDOREDUCTASE FROM AGROBACTERIUM RADIOBACTER TITLE 2 IN COMPLEX WITH NAD+, R-2,3-DIHYDROXYISOVALERATE 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: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OXIDOREDUCTASE, R-2, 3-DIHYDROXYISOVALERATE 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 5UIA 1 LINK REVDAT 4 01-JAN-20 5UIA 1 REMARK REVDAT 3 20-SEP-17 5UIA 1 REMARK REVDAT 2 07-JUN-17 5UIA 1 AUTHOR REVDAT 1 01-FEB-17 5UIA 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+, R-2,3-DIHYDROXYISOVALERATE JRNL TITL 3 AND MAGNESIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.18 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 47163 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2463 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) : 2.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3223 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.3430 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5158 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.89000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : 1.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.24000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.160 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.381 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5378 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4905 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7319 ; 1.233 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11322 ; 0.897 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 682 ; 5.803 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 226 ;35.537 ;23.894 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 826 ;12.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;12.751 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 832 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6025 ; 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): 2737 ; 1.661 ; 3.199 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2734 ; 1.659 ; 3.196 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3414 ; 2.541 ; 4.789 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3414 ; 2.538 ; 4.788 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2641 ; 2.016 ; 3.439 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2642 ; 2.016 ; 3.441 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3906 ; 3.139 ; 5.085 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5764 ; 4.615 ;37.991 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5757 ; 4.606 ;37.954 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): 18.0612 -31.3398 15.3787 REMARK 3 T TENSOR REMARK 3 T11: 0.2031 T22: 0.1310 REMARK 3 T33: 0.0071 T12: -0.0728 REMARK 3 T13: -0.0085 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.4944 L22: 0.9966 REMARK 3 L33: 1.2842 L12: 0.1702 REMARK 3 L13: -0.1288 L23: 0.5792 REMARK 3 S TENSOR REMARK 3 S11: 0.1408 S12: -0.1101 S13: 0.0319 REMARK 3 S21: 0.1835 S22: -0.1115 S23: -0.0421 REMARK 3 S31: 0.0965 S32: 0.1140 S33: -0.0293 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): 24.4245 -56.2659 -19.7216 REMARK 3 T TENSOR REMARK 3 T11: 0.2127 T22: 0.1900 REMARK 3 T33: 0.0114 T12: 0.1292 REMARK 3 T13: -0.0295 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 0.6094 L22: 1.2360 REMARK 3 L33: 0.7118 L12: -0.7805 REMARK 3 L13: -0.4187 L23: 0.5294 REMARK 3 S TENSOR REMARK 3 S11: 0.1780 S12: 0.2213 S13: -0.0394 REMARK 3 S21: -0.1471 S22: -0.1970 S23: 0.0058 REMARK 3 S31: 0.0785 S32: -0.0101 S33: 0.0189 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 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 5UIA 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_1000225885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-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 0.5.29 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49821 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 29.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.03700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 69.20550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.96300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.20550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 56.96300 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: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 LYS A 28 CD CE NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 207 O CE NZ 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 ARG A 337 CD NE CZ NH1 NH2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 GLU B 53 CG CD OE1 OE2 REMARK 470 GLU B 170 CG CD OE1 OE2 REMARK 470 GLU B 172 CG CD OE1 OE2 REMARK 470 LYS B 209 CG CD CE NZ REMARK 470 GLN B 279 CG CD OE1 NE2 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 -86.39 -127.58 REMARK 500 PRO A 242 51.80 -118.98 REMARK 500 THR A 314 48.24 -101.17 REMARK 500 CYS B 13 48.30 -86.54 REMARK 500 PHE B 174 -89.60 -123.54 REMARK 500 PRO B 242 63.40 -117.12 REMARK 500 THR B 314 56.93 -104.76 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 78.6 REMARK 620 3 VAL A 27 O 109.8 94.1 REMARK 620 4 ALA A 30 O 91.8 168.0 96.0 REMARK 620 5 HOH A 563 O 158.7 88.0 87.4 98.9 REMARK 620 6 HOH A 564 O 90.0 82.6 159.0 90.2 71.8 REMARK 620 N 1 2 3 4 5 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 77.6 REMARK 620 3 VAL B 27 O 97.1 89.6 REMARK 620 4 ALA B 30 O 89.1 165.0 85.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 89V 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 89V 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 R-2,3-DIHYDROXYISOVALERATE REMARK 900 RELATED ID: 5UHZ RELATED DB: PDB REMARK 900 RELATED ID: 5UI9 RELATED DB: PDB REMARK 900 RELATED ID: 5UIA RELATED DB: PDB REMARK 900 RELATED ID: 5UIB RELATED DB: PDB DBREF 5UIA A 1 345 UNP B9JK80 B9JK80_AGRRK 1 345 DBREF 5UIA 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 89V A 402 9 HET MG A 403 1 HET NAD B 401 44 HET 89V B 402 9 HET MG B 403 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 89V (2S)-2,3-DIHYDROXY-3-METHYLBUTANOIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 89V 2(C5 H10 O4) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *125(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 GLN A 78 5 3 HELIX 5 AA5 SER A 79 HIS A 90 1 12 HELIX 6 AA6 SER A 103 ALA A 117 1 15 HELIX 7 AA7 ASN A 126 TRP A 129 5 4 HELIX 8 AA8 GLN A 130 GLY A 143 1 14 HELIX 9 AA9 GLN A 165 GLU A 170 5 6 HELIX 10 AB1 PHE A 174 LEU A 179 1 6 HELIX 11 AB2 LEU A 179 GLY A 192 1 14 HELIX 12 AB3 TRP A 288 GLY A 309 1 22 HELIX 13 AB4 SER A 315 GLY A 336 1 22 HELIX 14 AB5 GLY A 342 LEU A 345 5 4 HELIX 15 AB6 GLY B 14 VAL B 27 1 14 HELIX 16 AB7 ASP B 39 GLY B 51 1 13 HELIX 17 AB8 ASP B 58 GLY B 66 1 9 HELIX 18 AB9 THR B 76 GLN B 78 5 3 HELIX 19 AC1 SER B 79 HIS B 90 1 12 HELIX 20 AC2 SER B 103 ASP B 118 1 16 HELIX 21 AC3 ASN B 126 TRP B 129 5 4 HELIX 22 AC4 GLN B 130 SER B 142 1 13 HELIX 23 AC5 GLN B 165 GLU B 170 5 6 HELIX 24 AC6 PHE B 174 LEU B 179 1 6 HELIX 25 AC7 LEU B 179 GLY B 192 1 14 HELIX 26 AC8 TRP B 288 GLY B 309 1 22 HELIX 27 AC9 SER B 315 GLY B 336 1 22 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 GLN A 97 1 O ILE A 95 N ILE A 73 SHEET 6 AA1 6 LEU A 121 HIS A 124 1 O HIS A 124 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 ARG A 256 O GLU A 264 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 LEU A 218 O SER A 226 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 TYR B 56 SHEET 3 AA3 6 LEU B 6 ILE B 11 1 N GLY B 8 O GLY B 31 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 GLY B 267 O GLY B 270 SHEET 3 AA4 9 GLY B 253 SER B 258 -1 N SER B 258 O ARG B 262 SHEET 4 AA4 9 LEU B 245 GLY B 250 -1 N GLY B 250 O GLY B 253 SHEET 5 AA4 9 PRO B 148 ARG B 156 -1 N SER B 154 O LEU B 245 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 ALA B 214 O VAL B 230 SHEET 8 AA4 9 VAL B 194 LYS B 202 -1 N THR B 198 O LEU B 217 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 2.29 LINK O LYS A 25 MG MG A 403 1555 1555 2.85 LINK O VAL A 27 MG MG A 403 1555 1555 2.38 LINK O ALA A 30 MG MG A 403 1555 1555 2.27 LINK MG MG A 403 O HOH A 563 1555 1555 2.35 LINK MG MG A 403 O HOH A 564 1555 1555 2.43 LINK O TRP B 24 MG MG B 403 1555 1555 2.46 LINK O LYS B 25 MG MG B 403 1555 1555 2.90 LINK O VAL B 27 MG MG B 403 1555 1555 2.58 LINK O ALA B 30 MG MG B 403 1555 1555 2.31 CISPEP 1 LYS A 98 PRO A 99 0 -17.30 CISPEP 2 PHE A 241 PRO A 242 0 3.90 CISPEP 3 ARG A 286 PRO A 287 0 3.30 CISPEP 4 LYS B 98 PRO B 99 0 -11.56 CISPEP 5 PHE B 241 PRO B 242 0 -3.87 CISPEP 6 ARG B 286 PRO B 287 0 -0.58 SITE 1 AC1 24 GLY A 12 GLY A 14 PHE A 15 PHE A 16 SITE 2 AC1 24 ASP A 37 ARG A 38 ASP A 39 ALA A 74 SITE 3 AC1 24 THR A 75 SER A 79 GLN A 97 LYS A 98 SITE 4 AC1 24 PRO A 99 ASN A 126 GLN A 165 TYR A 167 SITE 5 AC1 24 89V A 402 HOH A 508 HOH A 514 HOH A 521 SITE 6 AC1 24 HOH A 531 HOH A 545 HOH A 546 HOH A 547 SITE 1 AC2 8 LYS A 98 PHE A 127 VAL A 161 GLN A 165 SITE 2 AC2 8 ASP A 178 HIS A 182 TYR A 232 NAD A 401 SITE 1 AC3 6 TRP A 24 LYS A 25 VAL A 27 ALA A 30 SITE 2 AC3 6 HOH A 563 HOH A 564 SITE 1 AC4 21 GLY B 12 GLY B 14 PHE B 15 PHE B 16 SITE 2 AC4 21 ASP B 37 ARG B 38 ALA B 74 THR B 75 SITE 3 AC4 21 THR B 76 SER B 79 GLN B 97 LYS B 98 SITE 4 AC4 21 PRO B 99 ASN B 126 GLN B 165 TYR B 167 SITE 5 AC4 21 ILE B 291 89V B 402 HOH B 505 HOH B 514 SITE 6 AC4 21 HOH B 539 SITE 1 AC5 7 LYS B 98 PHE B 127 GLN B 165 ASP B 178 SITE 2 AC5 7 HIS B 182 TYR B 232 NAD B 401 SITE 1 AC6 5 GLU B 5 TRP B 24 LYS B 25 VAL B 27 SITE 2 AC6 5 ALA B 30 CRYST1 138.411 113.926 65.719 90.00 95.10 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 0.007225 0.000000 0.000645 0.00000 SCALE2 0.000000 0.008778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015277 0.00000