HEADER MEMBRANE TRANSPORT 07-NOV-06 2J9C TITLE STRUCTURE OF GLNK1 WITH BOUND EFFECTORS INDICATES REGULATORY MECHANISM TITLE 2 FOR AMMONIA UPTAKE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL NITROGEN REGULATORY PII-LIKE PROTEIN MJ0059; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: GLNK1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 STRAIN: AMJFT37; SOURCE 5 ATCC: 625482; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-D2 KEYWDS EM SINGLE PARTICLE, NITROGEN METABOLISM, SIGNALLING, TRANSCRIPTION, KEYWDS 2 MEMBRANE TRANSPORT, HYPOTHETICAL PROTEIN, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR O.YILDIZ,C.KALTHOFF,S.RAUNSER,W.KUEHLBRANDT REVDAT 3 13-DEC-23 2J9C 1 LINK REVDAT 2 24-FEB-09 2J9C 1 VERSN REVDAT 1 16-JAN-07 2J9C 0 JRNL AUTH O.YILDIZ,C.KALTHOFF,S.RAUNSER,W.KUHLBRANDT JRNL TITL STRUCTURE OF GLNK1 WITH BOUND EFFECTORS INDICATES REGULATORY JRNL TITL 2 MECHANISM FOR AMMONIA UPTAKE. JRNL REF EMBO J. V. 26 589 2007 JRNL REFN ISSN 0261-4189 JRNL PMID 17203075 JRNL DOI 10.1038/SJ.EMBOJ.7601492 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 91351 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4808 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6733 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 354 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2736 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 487 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.048 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.573 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2972 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2104 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4023 ; 2.068 ; 2.043 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5174 ; 1.109 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 6.728 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;37.199 ;24.298 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 594 ;14.189 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.437 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 465 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3173 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 535 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 553 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2362 ; 0.222 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1392 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1668 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 342 ; 0.216 ; 0.200 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): 16 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.309 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.226 ; 0.200 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): 2331 ; 3.988 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2918 ; 4.364 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1325 ; 5.740 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1091 ; 7.357 ; 8.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2J9C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1290030445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.071 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.330 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1GNK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.85000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.85000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.85000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS B 116 REMARK 465 HIS B 117 REMARK 465 HIS C 116 REMARK 465 HIS C 117 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 NZ LYS A 105 O HOH A 2167 1.87 REMARK 500 OE1 GLU C 107 O HOH C 2138 1.93 REMARK 500 O HOH B 2009 O HOH B 2015 1.98 REMARK 500 OD1 ASP C 71 O HOH C 2095 1.98 REMARK 500 OE2 GLU A 62 O HOH A 2119 1.98 REMARK 500 O HOH B 2150 O HOH C 2146 2.00 REMARK 500 OE2 GLU C 5 O HOH C 2006 2.03 REMARK 500 NE2 GLN B 39 O HOH B 2064 2.08 REMARK 500 O HOH B 2076 O HOH B 2081 2.10 REMARK 500 NZ LYS A 105 O HOH A 2166 2.11 REMARK 500 OH TYR B 46 O HOH B 2076 2.14 REMARK 500 NE ARG C 98 O HOH C 2138 2.16 REMARK 500 OE2 GLU B 14 O HOH B 2029 2.17 REMARK 500 O HOH A 2103 O HOH A 2113 2.17 REMARK 500 OE1 GLU C 32 O1 EDO C 1119 2.19 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 C 45 OD1 ASN C 72 4664 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 5 CD GLU B 5 OE1 -0.067 REMARK 500 GLU C 107 CB GLU C 107 CG -0.139 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 49 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU B 63 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG B 101 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 101 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG C 45 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG C 49 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG C 98 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ARG A 47 54.95 37.78 REMARK 500 ILE A 52 -60.90 -129.84 REMARK 500 TYR B 51 72.47 -118.19 REMARK 500 ARG C 49 89.41 -5.05 REMARK 500 GLU C 50 114.31 143.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG C 49 GLU C 50 124.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2012 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A2035 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH C2004 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH C2021 DISTANCE = 6.95 ANGSTROMS 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 A1117 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A1116 O3G REMARK 620 2 ATP A1116 O2B 92.0 REMARK 620 3 ATP A1116 O1A 86.5 86.5 REMARK 620 4 HOH A2077 O 176.5 88.4 97.0 REMARK 620 5 HOH A2090 O 94.6 173.4 93.6 85.0 REMARK 620 6 HOH A2177 O 87.7 87.0 171.1 88.8 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1117 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP B1116 O1A REMARK 620 2 ATP B1116 O3G 92.0 REMARK 620 3 ATP B1116 O2B 88.5 88.9 REMARK 620 4 HOH B2062 O 94.1 172.6 87.2 REMARK 620 5 HOH B2065 O 178.6 89.5 91.7 84.4 REMARK 620 6 HOH B2070 O 91.2 95.4 175.7 88.5 88.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1117 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP C1116 O2G REMARK 620 2 ATP C1116 O1A 88.1 REMARK 620 3 ATP C1116 O2B 88.0 86.7 REMARK 620 4 HOH C2061 O 175.2 96.1 89.9 REMARK 620 5 HOH C2071 O 96.0 91.5 175.6 86.2 REMARK 620 6 HOH C2145 O 87.9 175.7 91.4 87.8 90.6 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1118 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1119 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1121 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A1122 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B1118 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C1117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C1118 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1119 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP C1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C1119 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2J9D RELATED DB: PDB REMARK 900 STRUCTURE OF GLNK1 WITH BOUND EFFECTORS INDICATES REGULATORY REMARK 900 MECHANISM FOR AMMONIA UPTAKE REMARK 900 RELATED ID: 2J9E RELATED DB: PDB REMARK 900 STRUCTURE OF GLNK1 WITH BOUND EFFECTORS INDICATES REGULATORY REMARK 900 MECHANISM FOR AMMONIA UPTAKE DBREF 2J9C A -1 0 PDB 2J9C 2J9C -1 0 DBREF 2J9C A 1 112 UNP Q60381 Y059_METJA 1 112 DBREF 2J9C A 113 117 PDB 2J9C 2J9C 113 117 DBREF 2J9C B -1 0 PDB 2J9C 2J9C -1 0 DBREF 2J9C B 1 112 UNP Q60381 Y059_METJA 1 112 DBREF 2J9C B 113 117 PDB 2J9C 2J9C 113 117 DBREF 2J9C C -1 0 PDB 2J9C 2J9C -1 0 DBREF 2J9C C 1 112 UNP Q60381 Y059_METJA 1 112 DBREF 2J9C C 113 117 PDB 2J9C 2J9C 113 117 SEQRES 1 A 119 GLY SER MET LYS LYS VAL GLU ALA ILE ILE ARG PRO GLU SEQRES 2 A 119 LYS LEU GLU ILE VAL LYS LYS ALA LEU SER ASP ALA GLY SEQRES 3 A 119 TYR VAL GLY MET THR VAL SER GLU VAL LYS GLY ARG GLY SEQRES 4 A 119 VAL GLN GLY GLY ILE VAL GLU ARG TYR ARG GLY ARG GLU SEQRES 5 A 119 TYR ILE VAL ASP LEU ILE PRO LYS VAL LYS ILE GLU LEU SEQRES 6 A 119 VAL VAL LYS GLU GLU ASP VAL ASP ASN VAL ILE ASP ILE SEQRES 7 A 119 ILE CYS GLU ASN ALA ARG THR GLY ASN PRO GLY ASP GLY SEQRES 8 A 119 LYS ILE PHE VAL ILE PRO VAL GLU ARG VAL VAL ARG VAL SEQRES 9 A 119 ARG THR LYS GLU GLU GLY LYS GLU ALA LEU LEU GLU HIS SEQRES 10 A 119 HIS HIS SEQRES 1 B 119 GLY SER MET LYS LYS VAL GLU ALA ILE ILE ARG PRO GLU SEQRES 2 B 119 LYS LEU GLU ILE VAL LYS LYS ALA LEU SER ASP ALA GLY SEQRES 3 B 119 TYR VAL GLY MET THR VAL SER GLU VAL LYS GLY ARG GLY SEQRES 4 B 119 VAL GLN GLY GLY ILE VAL GLU ARG TYR ARG GLY ARG GLU SEQRES 5 B 119 TYR ILE VAL ASP LEU ILE PRO LYS VAL LYS ILE GLU LEU SEQRES 6 B 119 VAL VAL LYS GLU GLU ASP VAL ASP ASN VAL ILE ASP ILE SEQRES 7 B 119 ILE CYS GLU ASN ALA ARG THR GLY ASN PRO GLY ASP GLY SEQRES 8 B 119 LYS ILE PHE VAL ILE PRO VAL GLU ARG VAL VAL ARG VAL SEQRES 9 B 119 ARG THR LYS GLU GLU GLY LYS GLU ALA LEU LEU GLU HIS SEQRES 10 B 119 HIS HIS SEQRES 1 C 119 GLY SER MET LYS LYS VAL GLU ALA ILE ILE ARG PRO GLU SEQRES 2 C 119 LYS LEU GLU ILE VAL LYS LYS ALA LEU SER ASP ALA GLY SEQRES 3 C 119 TYR VAL GLY MET THR VAL SER GLU VAL LYS GLY ARG GLY SEQRES 4 C 119 VAL GLN GLY GLY ILE VAL GLU ARG TYR ARG GLY ARG GLU SEQRES 5 C 119 TYR ILE VAL ASP LEU ILE PRO LYS VAL LYS ILE GLU LEU SEQRES 6 C 119 VAL VAL LYS GLU GLU ASP VAL ASP ASN VAL ILE ASP ILE SEQRES 7 C 119 ILE CYS GLU ASN ALA ARG THR GLY ASN PRO GLY ASP GLY SEQRES 8 C 119 LYS ILE PHE VAL ILE PRO VAL GLU ARG VAL VAL ARG VAL SEQRES 9 C 119 ARG THR LYS GLU GLU GLY LYS GLU ALA LEU LEU GLU HIS SEQRES 10 C 119 HIS HIS HET ATP A1116 31 HET MG A1117 1 HET CL A1118 1 HET CL A1119 1 HET EDO A1120 4 HET ACT A1121 4 HET ACT A1122 4 HET ATP B1116 31 HET MG B1117 1 HET CL B1118 1 HET EDO B1119 4 HET EDO B1120 4 HET ATP C1116 31 HET MG C1117 1 HET CL C1118 1 HET EDO C1119 4 HET ACT C1120 4 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 4 ATP 3(C10 H16 N5 O13 P3) FORMUL 5 MG 3(MG 2+) FORMUL 6 CL 4(CL 1-) FORMUL 8 EDO 4(C2 H6 O2) FORMUL 9 ACT 3(C2 H3 O2 1-) FORMUL 21 HOH *487(H2 O) HELIX 1 1 LYS A 12 ALA A 23 1 12 HELIX 2 2 ASP A 69 ARG A 82 1 14 HELIX 3 3 GLY A 108 LEU A 113 5 6 HELIX 4 4 LYS B 12 ALA B 23 1 12 HELIX 5 5 ASP B 69 ARG B 82 1 14 HELIX 6 6 GLY B 108 LEU B 113 5 6 HELIX 7 7 LYS C 12 ALA C 23 1 12 HELIX 8 8 ASP C 69 ARG C 82 1 14 HELIX 9 9 GLY C 108 LEU C 113 5 6 SHEET 1 AA 6 ARG A 98 ARG A 101 0 SHEET 2 AA 6 GLY B 89 VAL B 96 -1 O ILE B 91 N VAL A 100 SHEET 3 AA 6 MET B 1 ILE B 8 -1 O MET B 1 N VAL B 96 SHEET 4 AA 6 ILE B 56 LYS B 66 -1 O VAL B 59 N ILE B 8 SHEET 5 AA 6 MET B 28 ARG B 36 -1 O THR B 29 N GLU B 62 SHEET 6 AA 6 MET A 28 ARG A 36 1 O MET A 28 N ARG B 36 SHEET 1 AB 6 ARG A 98 ARG A 101 0 SHEET 2 AB 6 GLY B 89 VAL B 96 -1 O ILE B 91 N VAL A 100 SHEET 3 AB 6 MET B 1 ILE B 8 -1 O MET B 1 N VAL B 96 SHEET 4 AB 6 ILE B 56 LYS B 66 -1 O VAL B 59 N ILE B 8 SHEET 5 AB 6 MET B 28 ARG B 36 -1 O THR B 29 N GLU B 62 SHEET 6 AB 6 MET C 28 ARG C 36 -1 O LYS C 34 N VAL B 30 SHEET 1 AC 2 ARG A 45 TYR A 46 0 SHEET 2 AC 2 ARG A 49 GLU A 50 -1 O ARG A 49 N TYR A 46 SHEET 1 BA 2 ARG B 45 TYR B 46 0 SHEET 2 BA 2 ARG B 49 GLU B 50 -1 O ARG B 49 N TYR B 46 LINK O3G ATP A1116 MG MG A1117 1555 1555 1.98 LINK O2B ATP A1116 MG MG A1117 1555 1555 2.04 LINK O1A ATP A1116 MG MG A1117 1555 1555 2.08 LINK MG MG A1117 O HOH A2077 1555 1555 2.04 LINK MG MG A1117 O HOH A2090 1555 1555 2.10 LINK MG MG A1117 O HOH A2177 1555 1555 2.12 LINK O1A ATP B1116 MG MG B1117 1555 1555 2.05 LINK O3G ATP B1116 MG MG B1117 1555 1555 1.98 LINK O2B ATP B1116 MG MG B1117 1555 1555 2.07 LINK MG MG B1117 O HOH B2062 1555 1555 2.10 LINK MG MG B1117 O HOH B2065 1555 1555 2.15 LINK MG MG B1117 O HOH B2070 1555 1555 2.08 LINK O2G ATP C1116 MG MG C1117 1555 1555 2.03 LINK O1A ATP C1116 MG MG C1117 1555 1555 2.08 LINK O2B ATP C1116 MG MG C1117 1555 1555 2.06 LINK MG MG C1117 O HOH C2061 1555 1555 2.13 LINK MG MG C1117 O HOH C2071 1555 1555 2.09 LINK MG MG C1117 O HOH C2145 1555 1555 2.09 CISPEP 1 GLY B -1 SER B 0 0 4.20 SITE 1 AC1 4 ATP A1116 HOH A2077 HOH A2090 HOH A2177 SITE 1 AC2 3 LYS A 3 LYS B 3 LYS C 3 SITE 1 AC3 3 LYS A 18 GLU A 107 HOH A2170 SITE 1 AC4 8 SER A 31 GLU A 32 VAL A 33 ACT A1122 SITE 2 AC4 8 SER B 31 GLU B 32 SER C 31 GLU C 32 SITE 1 AC5 7 SER A 31 LYS A 60 ACT A1121 SER B 31 SITE 2 AC5 7 LYS B 60 SER C 31 LYS C 60 SITE 1 AC6 4 ATP B1116 HOH B2062 HOH B2065 HOH B2070 SITE 1 AC7 4 LEU A 112 VAL B 38 LYS B 90 ATP B1116 SITE 1 AC8 4 ATP C1116 HOH C2061 HOH C2071 HOH C2145 SITE 1 AC9 3 VAL A 70 ARG C 98 HOH C2055 SITE 1 BC1 4 LYS C 34 TYR C 51 PRO C 57 HOH C2077 SITE 1 BC2 26 ILE A 7 GLY A 35 ARG A 36 GLY A 37 SITE 2 BC2 26 VAL A 38 LYS A 58 PRO A 86 GLY A 87 SITE 3 BC2 26 ASP A 88 GLY A 89 LYS A 90 MG A1117 SITE 4 BC2 26 HOH A2077 HOH A2090 HOH A2091 HOH A2175 SITE 5 BC2 26 HOH A2176 HOH A2177 HOH A2178 MET C 28 SITE 6 BC2 26 THR C 29 GLU C 62 VAL C 64 ARG C 101 SITE 7 BC2 26 ARG C 103 HIS C 115 SITE 1 BC3 4 GLN A 39 HOH A2179 SER C 21 HOH C2032 SITE 1 BC4 27 GLY A 27 MET A 28 THR A 29 GLU A 62 SITE 2 BC4 27 VAL A 64 ARG A 101 ARG A 103 HIS A 115 SITE 3 BC4 27 ILE B 7 GLY B 35 ARG B 36 GLY B 37 SITE 4 BC4 27 VAL B 38 LYS B 58 PRO B 86 GLY B 87 SITE 5 BC4 27 ASP B 88 GLY B 89 LYS B 90 MG B1117 SITE 6 BC4 27 CL B1118 HOH B2062 HOH B2065 HOH B2070 SITE 7 BC4 27 HOH B2072 HOH B2153 HOH B2154 SITE 1 BC5 5 ARG B 103 HOH B2155 ARG C 82 GLY C 84 SITE 2 BC5 5 HOH C2091 SITE 1 BC6 5 LYS B 105 HOH B2157 HOH B2158 GLU C 14 SITE 2 BC6 5 HOH C2015 SITE 1 BC7 26 GLY B 27 MET B 28 THR B 29 GLU B 62 SITE 2 BC7 26 VAL B 64 ARG B 101 ARG B 103 HIS B 115 SITE 3 BC7 26 ILE C 7 GLY C 35 ARG C 36 GLY C 37 SITE 4 BC7 26 VAL C 38 LYS C 58 PRO C 86 GLY C 87 SITE 5 BC7 26 ASP C 88 GLY C 89 LYS C 90 MG C1117 SITE 6 BC7 26 HOH C2061 HOH C2071 HOH C2144 HOH C2145 SITE 7 BC7 26 HOH C2146 HOH C2147 SITE 1 BC8 7 GLU C 32 VAL C 33 LYS C 34 LYS C 58 SITE 2 BC8 7 HOH C2148 HOH C2149 HOH C2150 CRYST1 122.700 122.700 45.700 90.00 90.00 120.00 P 63 18 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 0.008150 0.004705 0.000000 0.00000 SCALE2 0.000000 0.009411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021882 0.00000