HEADER TRANSFERASE 09-MAR-09 3GJU TITLE CRYSTAL STRUCTURE OF A PUTATIVE AMINOTRANSFERASE (MLL7127) FROM TITLE 2 MESORHIZOBIUM LOTI MAFF303099 AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AMINOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_TAXID: 266835; SOURCE 4 STRAIN: MAFF303099; SOURCE 5 GENE: MLL7127, NP_107505.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PYRIDOXAL PHOSPHATE, PLP-DEPENDENT TRANSFERASE-LIKE FOLD, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3GJU 1 REMARK SEQADV REVDAT 5 24-JUL-19 3GJU 1 REMARK LINK REVDAT 4 01-NOV-17 3GJU 1 REMARK REVDAT 3 13-JUL-11 3GJU 1 VERSN REVDAT 2 23-MAR-11 3GJU 1 HEADER TITLE KEYWDS REVDAT 1 17-MAR-09 3GJU 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (NP_107505.1) JRNL TITL 2 FROM MESORHIZOBIUM LOTI AT 1.55 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 61444 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3122 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3487 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 458 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 13.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3697 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2459 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5043 ; 1.533 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6008 ; 0.990 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 6.036 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.833 ;23.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 596 ;12.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.410 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4193 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 757 ; 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): 2311 ; 1.453 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 965 ; 0.471 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3709 ; 2.141 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1386 ; 3.723 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1318 ; 5.059 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 0 A 457 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4846 18.6939 21.9808 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: 0.0149 REMARK 3 T33: 0.0117 T12: 0.0010 REMARK 3 T13: 0.0047 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.2474 L22: 0.1991 REMARK 3 L33: 0.2405 L12: 0.0717 REMARK 3 L13: 0.0980 L23: -0.0059 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: 0.0212 S13: -0.0061 REMARK 3 S21: -0.0213 S22: 0.0229 S23: 0.0066 REMARK 3 S31: -0.0128 S32: -0.0289 S33: -0.0034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 2-METHYL- REMARK 3 2,4-PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION CONDITION HAS REMARK 3 BEEN MODELED IN THE SOLVENT STRUCTURE. 5. PYRIDOXAL PHOSPHATE IN REMARK 3 DUAL CONFORMATION AS FREE PLP AND COVALENTLY ATTACHED TO LYS289 REMARK 3 (LLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON REMARK 3 DIFFERENCE DENSITY AND OMIT MAPS AND STRUCTURAL SIMILARITY TO REMARK 3 PLP-DEPENDENT AMINOTRANSFERASES. 6. RESIDUE ALA288 IS PRESENT IN REMARK 3 THE VICINITY OF THE PUTATIVE ACTIVE SITE AND IS A RAMACHANDRAN REMARK 3 OUTLIER. THIS COULD HAVE SOME FUNCTIONAL SIGNIFICANCE. REMARK 4 REMARK 4 3GJU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162, 0.97941, 0.97954 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 28.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 59.1% 2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 0.1M BICINE PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 56.61200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.78850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.61200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.78850 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE REMARK 300 STABLE OLIGOMERIC FORM IN SOLUTION. 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: 10750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.6 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 57.70019 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.80363 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 496 LIES ON A SPECIAL POSITION. 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 ASN A 458 REMARK 465 LEU A 459 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 80 CD CE NZ REMARK 470 GLU A 142 CD OE1 OE2 REMARK 470 LYS A 281 CE NZ REMARK 470 ARG A 306 CD NE CZ NH1 NH2 REMARK 470 LYS A 453 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 276 O HOH A 918 2.09 REMARK 500 O HOH A 661 O HOH A 796 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 177 O HOH A 791 2656 2.13 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 LEU A 82 96.97 -162.69 REMARK 500 SER A 148 -163.03 -107.99 REMARK 500 PRO A 179 41.55 -103.49 REMARK 500 THR A 183 -168.17 -100.63 REMARK 500 ILE A 235 70.30 49.54 REMARK 500 ALA A 288 -144.31 -170.74 REMARK 500 ALA A 288 -144.44 -170.74 REMARK 500 LLP A 289 -97.38 37.92 REMARK 500 LYS A 289 -99.79 38.64 REMARK 500 MSE A 382 43.40 -96.38 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 PLP A 460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 462 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 390987 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3GJU A 1 459 UNP Q987B2 Q987B2_RHILO 1 459 SEQADV 3GJU GLY A 0 UNP Q987B2 EXPRESSION TAG SEQADV 3GJU LYS A 289 UNP Q987B2 LLP 289 MICROHETEROGENEITY SEQRES 1 A 460 GLY MSE LEU ASN GLN SER ASN GLU LEU ASN ALA TRP ASP SEQRES 2 A 460 ARG ASP HIS PHE PHE HIS PRO SER THR HIS MSE GLY THR SEQRES 3 A 460 HIS ALA ARG GLY GLU SER PRO THR ARG ILE MSE ALA GLY SEQRES 4 A 460 GLY GLU GLY VAL THR VAL TRP ASP ASN ASN GLY ARG LYS SEQRES 5 A 460 SER ILE ASP ALA PHE ALA GLY LEU TYR CYS VAL ASN VAL SEQRES 6 A 460 GLY TYR GLY ARG GLN LYS ILE ALA ASP ALA ILE ALA THR SEQRES 7 A 460 GLN ALA LYS ASN LEU ALA TYR TYR HIS ALA TYR VAL GLY SEQRES 8 A 460 HIS GLY THR GLU ALA SER ILE THR LEU ALA LYS MSE ILE SEQRES 9 A 460 ILE ASP ARG ALA PRO LYS GLY MSE SER ARG VAL TYR PHE SEQRES 10 A 460 GLY LEU SER GLY SER ASP ALA ASN GLU THR ASN ILE LYS SEQRES 11 A 460 LEU ILE TRP TYR TYR ASN ASN VAL LEU GLY ARG PRO GLU SEQRES 12 A 460 LYS LYS LYS ILE ILE SER ARG TRP ARG GLY TYR HIS GLY SEQRES 13 A 460 SER GLY VAL MSE THR GLY SER LEU THR GLY LEU ASP LEU SEQRES 14 A 460 PHE HIS ASN ALA PHE ASP LEU PRO ARG ALA PRO VAL LEU SEQRES 15 A 460 HIS THR GLU ALA PRO TYR TYR PHE ARG ARG THR ASP ARG SEQRES 16 A 460 SER MSE SER GLU GLU GLN PHE SER GLN HIS CYS ALA ASP SEQRES 17 A 460 LYS LEU GLU GLU MSE ILE LEU ALA GLU GLY PRO GLU THR SEQRES 18 A 460 ILE ALA ALA PHE ILE GLY GLU PRO ILE LEU GLY THR GLY SEQRES 19 A 460 GLY ILE VAL PRO PRO PRO ALA GLY TYR TRP GLU LYS ILE SEQRES 20 A 460 GLN ALA VAL LEU LYS LYS TYR ASP VAL LEU LEU VAL ALA SEQRES 21 A 460 ASP GLU VAL VAL THR GLY PHE GLY ARG LEU GLY THR MSE SEQRES 22 A 460 PHE GLY SER ASP HIS TYR GLY ILE LYS PRO ASP LEU ILE SEQRES 23 A 460 THR ILE ALA LLP GLY LEU THR SER ALA TYR ALA PRO LEU SEQRES 24 A 460 SER GLY VAL ILE VAL ALA ASP ARG VAL TRP GLN VAL LEU SEQRES 25 A 460 VAL GLN GLY SER ASP LYS LEU GLY SER LEU GLY HIS GLY SEQRES 26 A 460 TRP THR TYR SER ALA HIS PRO ILE CYS VAL ALA ALA GLY SEQRES 27 A 460 VAL ALA ASN LEU GLU LEU ILE ASP GLU MSE ASP LEU VAL SEQRES 28 A 460 THR ASN ALA GLY GLU THR GLY ALA TYR PHE ARG ALA GLU SEQRES 29 A 460 LEU ALA LYS ALA VAL GLY GLY HIS LYS ASN VAL GLY GLU SEQRES 30 A 460 VAL ARG GLY ASP GLY MSE LEU ALA ALA VAL GLU PHE VAL SEQRES 31 A 460 ALA ASP LYS ASP ASP ARG VAL PHE PHE ASP ALA SER GLN SEQRES 32 A 460 LYS ILE GLY PRO GLN VAL ALA THR ALA LEU ALA ALA SER SEQRES 33 A 460 GLY VAL ILE GLY ARG ALA MSE PRO GLN GLY ASP ILE LEU SEQRES 34 A 460 GLY PHE ALA PRO PRO LEU CYS LEU THR ARG GLU GLN ALA SEQRES 35 A 460 ASP ILE VAL VAL SER LYS THR ALA ASP ALA VAL LYS SER SEQRES 36 A 460 VAL PHE ALA ASN LEU MODRES 3GJU MSE A 1 MET SELENOMETHIONINE MODRES 3GJU MSE A 23 MET SELENOMETHIONINE MODRES 3GJU MSE A 36 MET SELENOMETHIONINE MODRES 3GJU MSE A 102 MET SELENOMETHIONINE MODRES 3GJU MSE A 111 MET SELENOMETHIONINE MODRES 3GJU MSE A 159 MET SELENOMETHIONINE MODRES 3GJU MSE A 196 MET SELENOMETHIONINE MODRES 3GJU MSE A 212 MET SELENOMETHIONINE MODRES 3GJU MSE A 272 MET SELENOMETHIONINE MODRES 3GJU LLP A 289 LYS MODRES 3GJU MSE A 347 MET SELENOMETHIONINE MODRES 3GJU MSE A 382 MET SELENOMETHIONINE MODRES 3GJU MSE A 422 MET SELENOMETHIONINE HET MSE A 1 13 HET MSE A 23 8 HET MSE A 36 13 HET MSE A 102 8 HET MSE A 111 13 HET MSE A 159 13 HET MSE A 196 8 HET MSE A 212 8 HET MSE A 272 8 HET LLP A 289 24 HET MSE A 347 8 HET MSE A 382 8 HET MSE A 422 8 HET PLP A 460 16 HET MPD A 461 8 HET MPD A 462 8 HETNAM MSE SELENOMETHIONINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 HOH *458(H2 O) HELIX 1 1 GLU A 7 PHE A 16 1 10 HELIX 2 2 HIS A 22 ARG A 28 1 7 HELIX 3 3 PHE A 56 CYS A 61 1 6 HELIX 4 4 ARG A 68 ALA A 83 1 16 HELIX 5 5 THR A 93 ALA A 107 1 15 HELIX 6 6 SER A 119 LEU A 138 1 20 HELIX 7 7 GLY A 157 THR A 164 1 8 HELIX 8 8 LEU A 166 HIS A 170 5 5 HELIX 9 9 TYR A 187 ARG A 191 5 5 HELIX 10 10 SER A 197 GLY A 217 1 21 HELIX 11 11 GLY A 241 TYR A 253 1 13 HELIX 12 12 PHE A 273 GLY A 279 1 7 HELIX 13 13 ALA A 288 THR A 292 5 5 HELIX 14 14 ASP A 305 GLY A 319 1 15 HELIX 15 15 HIS A 330 MSE A 347 1 18 HELIX 16 16 ASP A 348 GLY A 369 1 22 HELIX 17 17 ASP A 399 GLN A 402 5 4 HELIX 18 18 LYS A 403 SER A 415 1 13 HELIX 19 19 THR A 437 ALA A 457 1 21 SHEET 1 A 4 MSE A 36 GLU A 40 0 SHEET 2 A 4 THR A 43 ASP A 46 -1 O TRP A 45 N ALA A 37 SHEET 3 A 4 LYS A 51 ASP A 54 -1 O SER A 52 N VAL A 44 SHEET 4 A 4 VAL A 417 ILE A 418 1 O ILE A 418 N ILE A 53 SHEET 1 B 7 MSE A 111 GLY A 117 0 SHEET 2 B 7 SER A 299 ALA A 304 -1 O VAL A 303 N ARG A 113 SHEET 3 B 7 LEU A 284 ILE A 287 -1 N ILE A 285 O ILE A 302 SHEET 4 B 7 LEU A 256 ASP A 260 1 N ALA A 259 O LEU A 284 SHEET 5 B 7 ILE A 221 GLY A 226 1 N PHE A 224 O VAL A 258 SHEET 6 B 7 LYS A 145 ARG A 149 1 N ILE A 147 O ALA A 223 SHEET 7 B 7 VAL A 180 THR A 183 1 O LEU A 181 N SER A 148 SHEET 1 C 4 VAL A 374 ASP A 380 0 SHEET 2 C 4 LEU A 383 PHE A 388 -1 O GLU A 387 N GLU A 376 SHEET 3 C 4 ILE A 427 PHE A 430 -1 O LEU A 428 N VAL A 386 SHEET 4 C 4 ARG A 420 ALA A 421 -1 N ARG A 420 O GLY A 429 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LEU A 2 1555 1555 1.34 LINK C HIS A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N GLY A 24 1555 1555 1.34 LINK C ILE A 35 N MSE A 36 1555 1555 1.32 LINK C MSE A 36 N ALA A 37 1555 1555 1.33 LINK C LYS A 101 N MSE A 102 1555 1555 1.33 LINK C MSE A 102 N ILE A 103 1555 1555 1.32 LINK C GLY A 110 N MSE A 111 1555 1555 1.32 LINK C MSE A 111 N SER A 112 1555 1555 1.34 LINK C VAL A 158 N MSE A 159 1555 1555 1.34 LINK C MSE A 159 N THR A 160 1555 1555 1.32 LINK C SER A 195 N MSE A 196 1555 1555 1.34 LINK C MSE A 196 N SER A 197 1555 1555 1.32 LINK C GLU A 211 N MSE A 212 1555 1555 1.33 LINK C MSE A 212 N ILE A 213 1555 1555 1.33 LINK C THR A 271 N MSE A 272 1555 1555 1.32 LINK C MSE A 272 N PHE A 273 1555 1555 1.34 LINK C ALA A 288 N ALLP A 289 1555 1555 1.33 LINK C ALLP A 289 N GLY A 290 1555 1555 1.33 LINK C GLU A 346 N MSE A 347 1555 1555 1.33 LINK C MSE A 347 N ASP A 348 1555 1555 1.34 LINK C GLY A 381 N MSE A 382 1555 1555 1.34 LINK C MSE A 382 N LEU A 383 1555 1555 1.33 LINK C ALA A 421 N MSE A 422 1555 1555 1.32 LINK C MSE A 422 N PRO A 423 1555 1555 1.35 CISPEP 1 LEU A 175 PRO A 176 0 2.73 CISPEP 2 ALA A 178 PRO A 179 0 5.44 SITE 1 AC1 16 SER A 119 GLY A 120 SER A 121 TYR A 153 SITE 2 AC1 16 HIS A 154 GLY A 155 GLU A 227 ASP A 260 SITE 3 AC1 16 VAL A 262 VAL A 263 LLP A 289 THR A 326 SITE 4 AC1 16 HOH A 465 HOH A 491 HOH A 513 HOH A 530 SITE 1 AC2 4 LYS A 101 GLU A 244 LYS A 245 HOH A 485 SITE 1 AC3 6 LYS A 109 GLY A 110 ASP A 305 HOH A 509 SITE 2 AC3 6 HOH A 702 HOH A 774 CRYST1 113.224 59.577 85.337 90.00 130.59 90.00 C 1 2 1 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 0.008832 0.000000 0.007567 0.00000 SCALE2 0.000000 0.016785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015431 0.00000