HEADER OXIDOREDUCTASE 12-JAN-17 5UHW TITLE CRYSTAL STRUCTURE OF AN OXIDOREDUCTASE FROM AGROBACTERIUM RADIOBACTER TITLE 2 IN COMPLEX WITH NAD+ 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 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 5UHW 1 LINK REVDAT 4 01-JAN-20 5UHW 1 REMARK REVDAT 3 20-SEP-17 5UHW 1 REMARK REVDAT 2 07-JUN-17 5UHW 1 AUTHOR REVDAT 1 25-JAN-17 5UHW 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+ AND MAGNESIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.24 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 45754 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2394 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) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3146 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5194 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.201 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.730 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5398 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4951 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7336 ; 1.491 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11448 ; 0.962 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 682 ; 6.189 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;36.492 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 853 ;14.821 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;14.759 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 828 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6037 ; 0.005 ; 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 ; 0.863 ; 3.585 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2733 ; 0.864 ; 3.585 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3414 ; 1.535 ; 5.375 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3415 ; 1.535 ; 5.375 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2664 ; 0.799 ; 3.708 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2664 ; 0.799 ; 3.708 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3922 ; 1.401 ; 5.522 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5786 ; 2.743 ;41.925 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5786 ; 2.743 ;41.924 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): 18.0256 -30.8608 15.3351 REMARK 3 T TENSOR REMARK 3 T11: 0.0964 T22: 0.0915 REMARK 3 T33: 0.0321 T12: -0.0538 REMARK 3 T13: 0.0202 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 0.6033 L22: 1.0270 REMARK 3 L33: 1.4093 L12: 0.2705 REMARK 3 L13: -0.1447 L23: 0.6981 REMARK 3 S TENSOR REMARK 3 S11: 0.1540 S12: -0.1123 S13: 0.0328 REMARK 3 S21: 0.1462 S22: -0.1245 S23: -0.0467 REMARK 3 S31: 0.1020 S32: 0.0153 S33: -0.0295 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): 24.2895 -55.9229 -19.7201 REMARK 3 T TENSOR REMARK 3 T11: 0.1132 T22: 0.1865 REMARK 3 T33: 0.0763 T12: 0.0981 REMARK 3 T13: 0.0330 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 0.4546 L22: 1.7345 REMARK 3 L33: 0.8545 L12: -0.8493 REMARK 3 L13: -0.3038 L23: 0.6526 REMARK 3 S TENSOR REMARK 3 S11: 0.1216 S12: 0.1601 S13: -0.0004 REMARK 3 S21: -0.1082 S22: -0.1750 S23: 0.0142 REMARK 3 S31: 0.0502 S32: -0.0333 S33: 0.0533 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5UHW 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_1000225851. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-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 : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48152 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 19.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.76700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.3.02 REMARK 200 STARTING MODEL: 3EZY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 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 69.33700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.42800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.33700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 56.42800 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: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 209 CG CD CE NZ REMARK 470 ARG A 262 NE CZ NH1 NH2 REMARK 470 GLU B 53 CG CD OE1 OE2 REMARK 470 ARG B 112 NE CZ NH1 NH2 REMARK 470 GLU B 172 CG CD OE1 OE2 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 262 NE - CZ - NH1 ANGL. DEV. = 3.1 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 CYS A 13 53.58 -92.99 REMARK 500 PHE A 174 -83.38 -136.81 REMARK 500 LEU A 179 -55.07 -121.76 REMARK 500 THR A 314 50.45 -96.74 REMARK 500 CYS B 13 49.88 -95.55 REMARK 500 GLN B 165 89.78 -159.90 REMARK 500 PHE B 174 -85.82 -136.10 REMARK 500 ASN B 269 38.69 -95.86 REMARK 500 THR B 314 56.01 -101.71 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 24 O REMARK 620 2 LYS A 25 O 78.2 REMARK 620 3 VAL A 27 O 107.5 91.8 REMARK 620 4 ALA A 30 O 88.6 166.7 93.9 REMARK 620 5 HOH A 515 O 151.2 81.4 93.1 110.3 REMARK 620 6 HOH A 536 O 86.1 83.4 164.4 94.0 71.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 24 O REMARK 620 2 LYS B 25 O 76.0 REMARK 620 3 VAL B 27 O 98.1 87.1 REMARK 620 4 ALA B 30 O 95.2 169.1 87.9 REMARK 620 5 HOH B 527 O 92.1 86.5 166.3 100.3 REMARK 620 N 1 2 3 4 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 MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UHZ RELATED DB: PDB REMARK 900 RELATED ID: 5UIB RELATED DB: PDB REMARK 900 RELATED ID: 5UIA RELATED DB: PDB REMARK 900 RELATED ID: 5UI9 RELATED DB: PDB DBREF 5UHW A 1 345 UNP B9JK80 B9JK80_AGRRK 1 345 DBREF 5UHW 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 MG A 402 1 HET NAD B 401 44 HET MG B 402 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MG MAGNESIUM ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *63(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 SER A 142 1 13 HELIX 9 AA9 ASP A 160 GLN A 165 1 6 HELIX 10 AB1 PRO A 166 GLU A 170 5 5 HELIX 11 AB2 PHE A 174 LEU A 179 1 6 HELIX 12 AB3 LEU A 179 GLY A 192 1 14 HELIX 13 AB4 TRP A 288 GLY A 309 1 22 HELIX 14 AB5 SER A 315 GLY A 336 1 22 HELIX 15 AB6 ILE A 341 LEU A 345 1 5 HELIX 16 AB7 GLY B 14 VAL B 27 1 14 HELIX 17 AB8 ASP B 39 GLY B 51 1 13 HELIX 18 AB9 ASP B 58 GLY B 66 1 9 HELIX 19 AC1 THR B 76 GLN B 78 5 3 HELIX 20 AC2 SER B 79 HIS B 90 1 12 HELIX 21 AC3 SER B 103 ALA B 117 1 15 HELIX 22 AC4 ASN B 126 TRP B 129 5 4 HELIX 23 AC5 GLN B 130 SER B 142 1 13 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 ILE A 246 O LEU A 257 SHEET 5 AA2 9 PRO A 148 ARG A 156 -1 N TRP A 150 O ASP A 249 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 GLY B 8 O GLY B 31 SHEET 4 AA3 6 PHE B 70 ILE B 73 1 O ASP B 72 N ILE B 11 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 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 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 LEU B 218 O SER B 226 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 402 1555 1555 2.44 LINK O LYS A 25 MG MG A 402 1555 1555 2.69 LINK O VAL A 27 MG MG A 402 1555 1555 2.29 LINK O ALA A 30 MG MG A 402 1555 1555 2.24 LINK MG MG A 402 O HOH A 515 1555 1555 2.47 LINK MG MG A 402 O HOH A 536 1555 1555 2.61 LINK O TRP B 24 MG MG B 402 1555 1555 2.36 LINK O LYS B 25 MG MG B 402 1555 1555 2.84 LINK O VAL B 27 MG MG B 402 1555 1555 2.44 LINK O ALA B 30 MG MG B 402 1555 1555 2.38 LINK MG MG B 402 O HOH B 527 1555 1555 2.33 CISPEP 1 LYS A 98 PRO A 99 0 -17.25 CISPEP 2 PHE A 241 PRO A 242 0 6.97 CISPEP 3 ARG A 286 PRO A 287 0 3.57 CISPEP 4 LYS B 98 PRO B 99 0 -12.71 CISPEP 5 PHE B 241 PRO B 242 0 -1.55 CISPEP 6 ARG B 286 PRO B 287 0 -2.44 SITE 1 AC1 20 GLY A 12 GLY A 14 PHE A 15 PHE A 16 SITE 2 AC1 20 ASP A 37 ARG A 38 ASP A 39 ARG A 42 SITE 3 AC1 20 ALA A 74 THR A 75 SER A 79 GLN A 97 SITE 4 AC1 20 LYS A 98 PRO A 99 ASN A 126 GLN A 165 SITE 5 AC1 20 TYR A 167 HOH A 508 HOH A 524 HOH A 531 SITE 1 AC2 6 TRP A 24 LYS A 25 VAL A 27 ALA A 30 SITE 2 AC2 6 HOH A 515 HOH A 536 SITE 1 AC3 18 GLY B 12 GLY B 14 PHE B 15 PHE B 16 SITE 2 AC3 18 ASP B 37 ARG B 38 ASP B 39 ALA B 74 SITE 3 AC3 18 THR B 75 SER B 79 GLN B 97 LYS B 98 SITE 4 AC3 18 PRO B 99 ASN B 126 GLN B 165 HOH B 510 SITE 5 AC3 18 HOH B 517 HOH B 521 SITE 1 AC4 5 TRP B 24 LYS B 25 VAL B 27 ALA B 30 SITE 2 AC4 5 HOH B 527 CRYST1 138.674 112.856 65.741 90.00 95.02 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 0.007211 0.000000 0.000633 0.00000 SCALE2 0.000000 0.008861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015270 0.00000